PDB Short entry for 5C9Z HEADER TRANSFERASE/TRANSFERASE INHIBITOR 29-JUN-15 5C9Z TITLE CRYSTAL STRUCTURE OF PRMT5:MEP50 WITH EPZ015866 AND SINEFUNGIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ARGININE N-METHYLTRANSFERASE 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 72 KDA ICLN-BINDING PROTEIN,HISTONE-ARGININE N- COMPND 5 METHYLTRANSFERASE PRMT5,JAK-BINDING PROTEIN 1,SHK1 KINASE-BINDING COMPND 6 PROTEIN 1 HOMOLOG,SKB1HS; COMPND 7 EC: 2.1.1.-,2.1.1.125; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: METHYLOSOME PROTEIN 50; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: MEP-50,ANDROGEN RECEPTOR COFACTOR P44,WD REPEAT-CONTAINING COMPND 14 PROTEIN 77,P44/MEP50; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PRMT5, HRMT1L5, IBP72, JBP1, SKB1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PDEST; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: WDR77, MEP50, WD45, HKMT1069, NBLA10071; SOURCE 17 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 18 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 20 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PDEST KEYWDS METHYLTRANSFERASE PROTEIN-INHIBITOR COMPLEX, TRANSFERASE-TRANSFERASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.A.BORIACK-SJODIN REVDAT 1 29-JUN-16 5C9Z 0 JRNL AUTH P.A.BORIACK-SJODIN JRNL TITL CRYSTAL STRUCTURE OF PRMT5/MEP50 COMPLEX WITH SINEFUNGIN AND JRNL TITL 2 15866 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 82.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 49452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2659 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3660 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3970 REMARK 3 BIN FREE R VALUE SET COUNT : 180 REMARK 3 BIN FREE R VALUE : 0.4910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7427 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.46000 REMARK 3 B22 (A**2) : -1.22000 REMARK 3 B33 (A**2) : -5.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.365 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.274 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.268 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.182 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7781 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10609 ; 0.980 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 949 ; 5.410 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 359 ;34.968 ;23.928 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1244 ;15.694 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;16.376 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1162 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5985 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3793 ; 1.722 ; 6.045 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4740 ; 3.036 ; 9.062 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3987 ; 1.425 ; 6.076 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5C9Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000211279. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52114 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 REMARK 200 RESOLUTION RANGE LOW (A) : 89.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.60700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE, 0.1 M SODIUM REMARK 280 CITRATE PH 6.1, 10% W/V PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.40500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.89000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 89.45500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.40500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.89000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 89.45500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.40500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.89000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 89.45500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.40500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 68.89000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 89.45500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -7 REMARK 465 ASP A -6 REMARK 465 TYR A -5 REMARK 465 LYS A -4 REMARK 465 ASP A -3 REMARK 465 ASP A -2 REMARK 465 ASP A -1 REMARK 465 ASP A 0 REMARK 465 LYS A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 MET A 4 REMARK 465 ALA A 5 REMARK 465 VAL A 6 REMARK 465 GLY A 7 REMARK 465 GLY A 8 REMARK 465 ALA A 9 REMARK 465 GLY A 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 MET B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 HIS B 1 REMARK 465 ARG B 2 REMARK 465 LYS B 3 REMARK 465 GLU B 4 REMARK 465 THR B 5 REMARK 465 PRO B 6 REMARK 465 PRO B 7 REMARK 465 PRO B 8 REMARK 465 LEU B 9 REMARK 465 VAL B 10 REMARK 465 PRO B 11 REMARK 465 PRO B 12 REMARK 465 ALA B 13 REMARK 465 ALA B 14 REMARK 465 ARG B 15 REMARK 465 THR B 329 REMARK 465 GLU B 330 REMARK 465 PRO B 331 REMARK 465 LEU B 332 REMARK 465 PRO B 333 REMARK 465 ALA B 334 REMARK 465 PRO B 335 REMARK 465 GLY B 336 REMARK 465 PRO B 337 REMARK 465 ALA B 338 REMARK 465 SER B 339 REMARK 465 VAL B 340 REMARK 465 THR B 341 REMARK 465 GLU B 342 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU B 19 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 61 31.85 -93.15 REMARK 500 THR A 174 102.45 -47.38 REMARK 500 LEU A 222 21.05 -76.29 REMARK 500 GLU A 261 98.80 61.08 REMARK 500 GLU A 276 -178.47 -69.10 REMARK 500 ILE A 332 -37.24 -132.55 REMARK 500 GLU A 408 -63.04 -133.95 REMARK 500 ALA A 441 -71.30 64.37 REMARK 500 SER A 477 110.32 -168.91 REMARK 500 HIS A 507 -66.01 -136.25 REMARK 500 CYS A 518 -78.77 -115.47 REMARK 500 GLN A 561 -101.12 52.02 REMARK 500 THR A 629 -1.92 78.98 REMARK 500 ASN B 18 -71.50 -138.21 REMARK 500 LEU B 19 87.35 56.57 REMARK 500 ASN B 22 -22.84 76.75 REMARK 500 TRP B 54 79.18 -106.76 REMARK 500 ALA B 55 -157.85 -123.50 REMARK 500 PHE B 72 56.52 -98.56 REMARK 500 ILE B 147 -9.33 79.74 REMARK 500 ARG B 164 74.82 -106.64 REMARK 500 THR B 197 5.44 -68.93 REMARK 500 CYS B 208 -109.57 -79.45 REMARK 500 SER B 209 -70.61 -120.20 REMARK 500 SER B 225 18.26 -67.17 REMARK 500 CYS B 257 130.31 -36.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SFG A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4Z2 A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4X60 RELATED DB: PDB REMARK 900 4X60 CONTAINS THE PRMT5/MEP05/SINEFUNGIN COMPLEXED WITH A RELATED REMARK 900 COMPOUND, 15666. DBREF 5C9Z A 2 637 UNP O14744 ANM5_HUMAN 2 637 DBREF 5C9Z B 2 342 UNP Q9BQA1 MEP50_HUMAN 2 342 SEQADV 5C9Z MET A -7 UNP O14744 INITIATING METHIONINE SEQADV 5C9Z ASP A -6 UNP O14744 EXPRESSION TAG SEQADV 5C9Z TYR A -5 UNP O14744 EXPRESSION TAG SEQADV 5C9Z LYS A -4 UNP O14744 EXPRESSION TAG SEQADV 5C9Z ASP A -3 UNP O14744 EXPRESSION TAG SEQADV 5C9Z ASP A -2 UNP O14744 EXPRESSION TAG SEQADV 5C9Z ASP A -1 UNP O14744 EXPRESSION TAG SEQADV 5C9Z ASP A 0 UNP O14744 EXPRESSION TAG SEQADV 5C9Z LYS A 1 UNP O14744 EXPRESSION TAG SEQADV 5C9Z MET B -7 UNP Q9BQA1 INITIATING METHIONINE SEQADV 5C9Z HIS B -6 UNP Q9BQA1 EXPRESSION TAG SEQADV 5C9Z HIS B -5 UNP Q9BQA1 EXPRESSION TAG SEQADV 5C9Z HIS B -4 UNP Q9BQA1 EXPRESSION TAG SEQADV 5C9Z HIS B -3 UNP Q9BQA1 EXPRESSION TAG SEQADV 5C9Z HIS B -2 UNP Q9BQA1 EXPRESSION TAG SEQADV 5C9Z HIS B -1 UNP Q9BQA1 EXPRESSION TAG SEQADV 5C9Z HIS B 0 UNP Q9BQA1 EXPRESSION TAG SEQADV 5C9Z HIS B 1 UNP Q9BQA1 EXPRESSION TAG SEQRES 1 A 645 MET ASP TYR LYS ASP ASP ASP ASP LYS ALA ALA MET ALA SEQRES 2 A 645 VAL GLY GLY ALA GLY GLY SER ARG VAL SER SER GLY ARG SEQRES 3 A 645 ASP LEU ASN CYS VAL PRO GLU ILE ALA ASP THR LEU GLY SEQRES 4 A 645 ALA VAL ALA LYS GLN GLY PHE ASP PHE LEU CYS MET PRO SEQRES 5 A 645 VAL PHE HIS PRO ARG PHE LYS ARG GLU PHE ILE GLN GLU SEQRES 6 A 645 PRO ALA LYS ASN ARG PRO GLY PRO GLN THR ARG SER ASP SEQRES 7 A 645 LEU LEU LEU SER GLY ARG ASP TRP ASN THR LEU ILE VAL SEQRES 8 A 645 GLY LYS LEU SER PRO TRP ILE ARG PRO ASP SER LYS VAL SEQRES 9 A 645 GLU LYS ILE ARG ARG ASN SER GLU ALA ALA MET LEU GLN SEQRES 10 A 645 GLU LEU ASN PHE GLY ALA TYR LEU GLY LEU PRO ALA PHE SEQRES 11 A 645 LEU LEU PRO LEU ASN GLN GLU ASP ASN THR ASN LEU ALA SEQRES 12 A 645 ARG VAL LEU THR ASN HIS ILE HIS THR GLY HIS HIS SER SEQRES 13 A 645 SER MET PHE TRP MET ARG VAL PRO LEU VAL ALA PRO GLU SEQRES 14 A 645 ASP LEU ARG ASP ASP ILE ILE GLU ASN ALA PRO THR THR SEQRES 15 A 645 HIS THR GLU GLU TYR SER GLY GLU GLU LYS THR TRP MET SEQRES 16 A 645 TRP TRP HIS ASN PHE ARG THR LEU CYS ASP TYR SER LYS SEQRES 17 A 645 ARG ILE ALA VAL ALA LEU GLU ILE GLY ALA ASP LEU PRO SEQRES 18 A 645 SER ASN HIS VAL ILE ASP ARG TRP LEU GLY GLU PRO ILE SEQRES 19 A 645 LYS ALA ALA ILE LEU PRO THR SER ILE PHE LEU THR ASN SEQRES 20 A 645 LYS LYS GLY PHE PRO VAL LEU SER LYS MET HIS GLN ARG SEQRES 21 A 645 LEU ILE PHE ARG LEU LEU LYS LEU GLU VAL GLN PHE ILE SEQRES 22 A 645 ILE THR GLY THR ASN HIS HIS SER GLU LYS GLU PHE CYS SEQRES 23 A 645 SER TYR LEU GLN TYR LEU GLU TYR LEU SER GLN ASN ARG SEQRES 24 A 645 PRO PRO PRO ASN ALA TYR GLU LEU PHE ALA LYS GLY TYR SEQRES 25 A 645 GLU ASP TYR LEU GLN SER PRO LEU GLN PRO LEU MET ASP SEQRES 26 A 645 ASN LEU GLU SER GLN THR TYR GLU VAL PHE GLU LYS ASP SEQRES 27 A 645 PRO ILE LYS TYR SER GLN TYR GLN GLN ALA ILE TYR LYS SEQRES 28 A 645 CYS LEU LEU ASP ARG VAL PRO GLU GLU GLU LYS ASP THR SEQRES 29 A 645 ASN VAL GLN VAL LEU MET VAL LEU GLY ALA GLY ARG GLY SEQRES 30 A 645 PRO LEU VAL ASN ALA SER LEU ARG ALA ALA LYS GLN ALA SEQRES 31 A 645 ASP ARG ARG ILE LYS LEU TYR ALA VAL GLU LYS ASN PRO SEQRES 32 A 645 ASN ALA VAL VAL THR LEU GLU ASN TRP GLN PHE GLU GLU SEQRES 33 A 645 TRP GLY SER GLN VAL THR VAL VAL SER SER ASP MET ARG SEQRES 34 A 645 GLU TRP VAL ALA PRO GLU LYS ALA ASP ILE ILE VAL SER SEQRES 35 A 645 GLU LEU LEU GLY SER PHE ALA ASP ASN GLU LEU SER PRO SEQRES 36 A 645 GLU CYS LEU ASP GLY ALA GLN HIS PHE LEU LYS ASP ASP SEQRES 37 A 645 GLY VAL SER ILE PRO GLY GLU TYR THR SER PHE LEU ALA SEQRES 38 A 645 PRO ILE SER SER SER LYS LEU TYR ASN GLU VAL ARG ALA SEQRES 39 A 645 CYS ARG GLU LYS ASP ARG ASP PRO GLU ALA GLN PHE GLU SEQRES 40 A 645 MET PRO TYR VAL VAL ARG LEU HIS ASN PHE HIS GLN LEU SEQRES 41 A 645 SER ALA PRO GLN PRO CYS PHE THR PHE SER HIS PRO ASN SEQRES 42 A 645 ARG ASP PRO MET ILE ASP ASN ASN ARG TYR CYS THR LEU SEQRES 43 A 645 GLU PHE PRO VAL GLU VAL ASN THR VAL LEU HIS GLY PHE SEQRES 44 A 645 ALA GLY TYR PHE GLU THR VAL LEU TYR GLN ASP ILE THR SEQRES 45 A 645 LEU SER ILE ARG PRO GLU THR HIS SER PRO GLY MET PHE SEQRES 46 A 645 SER TRP PHE PRO ILE LEU PHE PRO ILE LYS GLN PRO ILE SEQRES 47 A 645 THR VAL ARG GLU GLY GLN THR ILE CYS VAL ARG PHE TRP SEQRES 48 A 645 ARG CYS SER ASN SER LYS LYS VAL TRP TYR GLU TRP ALA SEQRES 49 A 645 VAL THR ALA PRO VAL CYS SER ALA ILE HIS ASN PRO THR SEQRES 50 A 645 GLY ARG SER TYR THR ILE GLY LEU SEQRES 1 B 350 MET HIS HIS HIS HIS HIS HIS HIS HIS ARG LYS GLU THR SEQRES 2 B 350 PRO PRO PRO LEU VAL PRO PRO ALA ALA ARG GLU TRP ASN SEQRES 3 B 350 LEU PRO PRO ASN ALA PRO ALA CYS MET GLU ARG GLN LEU SEQRES 4 B 350 GLU ALA ALA ARG TYR ARG SER ASP GLY ALA LEU LEU LEU SEQRES 5 B 350 GLY ALA SER SER LEU SER GLY ARG CYS TRP ALA GLY SER SEQRES 6 B 350 LEU TRP LEU PHE LYS ASP PRO CYS ALA ALA PRO ASN GLU SEQRES 7 B 350 GLY PHE CYS SER ALA GLY VAL GLN THR GLU ALA GLY VAL SEQRES 8 B 350 ALA ASP LEU THR TRP VAL GLY GLU ARG GLY ILE LEU VAL SEQRES 9 B 350 ALA SER ASP SER GLY ALA VAL GLU LEU TRP GLU LEU ASP SEQRES 10 B 350 GLU ASN GLU THR LEU ILE VAL SER LYS PHE CYS LYS TYR SEQRES 11 B 350 GLU HIS ASP ASP ILE VAL SER THR VAL SER VAL LEU SER SEQRES 12 B 350 SER GLY THR GLN ALA VAL SER GLY SER LYS ASP ILE CYS SEQRES 13 B 350 ILE LYS VAL TRP ASP LEU ALA GLN GLN VAL VAL LEU SER SEQRES 14 B 350 SER TYR ARG ALA HIS ALA ALA GLN VAL THR CYS VAL ALA SEQRES 15 B 350 ALA SER PRO HIS LYS ASP SER VAL PHE LEU SER CYS SER SEQRES 16 B 350 GLU ASP ASN ARG ILE LEU LEU TRP ASP THR ARG CYS PRO SEQRES 17 B 350 LYS PRO ALA SER GLN ILE GLY CYS SER ALA PRO GLY TYR SEQRES 18 B 350 LEU PRO THR SER LEU ALA TRP HIS PRO GLN GLN SER GLU SEQRES 19 B 350 VAL PHE VAL PHE GLY ASP GLU ASN GLY THR VAL SER LEU SEQRES 20 B 350 VAL ASP THR LYS SER THR SER CYS VAL LEU SER SER ALA SEQRES 21 B 350 VAL HIS SER GLN CYS VAL THR GLY LEU VAL PHE SER PRO SEQRES 22 B 350 HIS SER VAL PRO PHE LEU ALA SER LEU SER GLU ASP CYS SEQRES 23 B 350 SER LEU ALA VAL LEU ASP SER SER LEU SER GLU LEU PHE SEQRES 24 B 350 ARG SER GLN ALA HIS ARG ASP PHE VAL ARG ASP ALA THR SEQRES 25 B 350 TRP SER PRO LEU ASN HIS SER LEU LEU THR THR VAL GLY SEQRES 26 B 350 TRP ASP HIS GLN VAL VAL HIS HIS VAL VAL PRO THR GLU SEQRES 27 B 350 PRO LEU PRO ALA PRO GLY PRO ALA SER VAL THR GLU HET SFG A 701 27 HET 4Z2 A 702 28 HET GOL A 703 6 HETNAM SFG SINEFUNGIN HETNAM 4Z2 2-(CYCLOBUTYLAMINO)-N-[(2S)-3-(3,4-DIHYDROISOQUINOLIN- HETNAM 2 4Z2 2(1H)-YL)-2-HYDROXYPROPYL]PYRIDINE-4-CARBOXAMIDE HETNAM GOL GLYCEROL HETSYN SFG ADENOSYL-ORNITHINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SFG C15 H23 N7 O5 FORMUL 4 4Z2 C22 H28 N4 O2 FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *123(H2 O) HELIX 1 AA1 GLU A 25 GLN A 36 1 12 HELIX 2 AA2 PRO A 58 ARG A 62 5 5 HELIX 3 AA3 SER A 69 LEU A 73 5 5 HELIX 4 AA4 SER A 74 LEU A 81 1 8 HELIX 5 AA5 VAL A 96 GLY A 118 1 23 HELIX 6 AA6 ASN A 131 HIS A 143 1 13 HELIX 7 AA7 ALA A 159 LEU A 163 5 5 HELIX 8 AA8 SER A 180 GLU A 182 5 3 HELIX 9 AA9 GLU A 183 CYS A 196 1 14 HELIX 10 AB1 SER A 214 ARG A 220 1 7 HELIX 11 AB2 SER A 234 PHE A 236 5 3 HELIX 12 AB3 SER A 247 GLU A 261 1 15 HELIX 13 AB4 PHE A 277 ASN A 290 1 14 HELIX 14 AB5 ASN A 295 ALA A 301 1 7 HELIX 15 AB6 GLU A 320 GLU A 328 1 9 HELIX 16 AB7 ILE A 332 VAL A 349 1 18 HELIX 17 AB8 PRO A 350 LYS A 354 5 5 HELIX 18 AB9 GLY A 369 LYS A 380 1 12 HELIX 19 AC1 ASN A 394 GLU A 408 1 15 HELIX 20 AC2 TRP A 409 SER A 411 5 3 HELIX 21 AC3 LEU A 445 GLY A 452 1 8 HELIX 22 AC4 ALA A 453 HIS A 455 5 3 HELIX 23 AC5 SER A 477 ALA A 486 1 10 HELIX 24 AC6 GLU A 495 MET A 500 5 6 HELIX 25 AC7 ARG A 568 HIS A 572 5 5 HELIX 26 AC8 ASN A 627 ARG A 631 5 5 HELIX 27 AC9 ASN B 69 CYS B 73 5 5 SHEET 1 AA1 9 SER A 16 ASP A 19 0 SHEET 2 AA1 9 PHE A 40 PRO A 44 1 O CYS A 42 N ARG A 18 SHEET 3 AA1 9 ILE A 82 LYS A 85 1 O VAL A 83 N LEU A 41 SHEET 4 AA1 9 ALA A 121 PRO A 125 1 O LEU A 123 N GLY A 84 SHEET 5 AA1 9 MET A 150 PRO A 156 1 O TRP A 152 N LEU A 124 SHEET 6 AA1 9 ILE A 202 GLU A 207 1 O ALA A 205 N MET A 153 SHEET 7 AA1 9 ILE A 226 PRO A 232 1 O ILE A 230 N LEU A 206 SHEET 8 AA1 9 GLN A 263 THR A 267 1 O ILE A 265 N LEU A 231 SHEET 9 AA1 9 SER A 16 ASP A 19 1 N ASP A 19 O ILE A 266 SHEET 1 AA2 2 LEU A 237 THR A 238 0 SHEET 2 AA2 2 PRO A 244 VAL A 245 -1 O VAL A 245 N LEU A 237 SHEET 1 AA3 5 VAL A 413 SER A 417 0 SHEET 2 AA3 5 ARG A 385 GLU A 392 1 N ALA A 390 O THR A 414 SHEET 3 AA3 5 VAL A 358 LEU A 364 1 N GLN A 359 O LYS A 387 SHEET 4 AA3 5 ALA A 429 VAL A 433 1 O VAL A 433 N MET A 362 SHEET 5 AA3 5 LEU A 457 ILE A 464 1 O ILE A 464 N ILE A 432 SHEET 1 AA4 5 TYR A 502 VAL A 503 0 SHEET 2 AA4 5 ILE A 582 VAL A 592 -1 O LEU A 583 N TYR A 502 SHEET 3 AA4 5 THR A 546 TYR A 560 -1 N LEU A 548 O ILE A 590 SHEET 4 AA4 5 GLU A 467 SER A 476 -1 N GLU A 467 O VAL A 558 SHEET 5 AA4 5 GLN A 516 SER A 522 -1 O PHE A 519 N SER A 470 SHEET 1 AA5 4 HIS A 510 GLN A 511 0 SHEET 2 AA5 4 GLU A 467 SER A 476 -1 N SER A 476 O HIS A 510 SHEET 3 AA5 4 THR A 546 TYR A 560 -1 O VAL A 558 N GLU A 467 SHEET 4 AA5 4 ILE A 563 SER A 566 -1 O ILE A 563 N TYR A 560 SHEET 1 AA6 4 ARG A 534 PRO A 541 0 SHEET 2 AA6 4 THR A 597 SER A 606 -1 O ILE A 598 N PHE A 540 SHEET 3 AA6 4 LYS A 610 ALA A 619 -1 O GLU A 614 N TRP A 603 SHEET 4 AA6 4 ILE A 635 GLY A 636 -1 O ILE A 635 N VAL A 611 SHEET 1 AA7 4 GLN B 30 TYR B 36 0 SHEET 2 AA7 4 LEU B 42 SER B 47 -1 O SER B 47 N GLN B 30 SHEET 3 AA7 4 GLY B 56 PHE B 61 -1 O TRP B 59 N LEU B 44 SHEET 4 AA7 4 ALA B 75 THR B 79 -1 O THR B 79 N GLY B 56 SHEET 1 AA8 4 VAL B 83 VAL B 89 0 SHEET 2 AA8 4 GLY B 93 SER B 98 -1 O GLY B 93 N VAL B 89 SHEET 3 AA8 4 ALA B 102 LEU B 108 -1 O TRP B 106 N ILE B 94 SHEET 4 AA8 4 ILE B 115 TYR B 122 -1 O LYS B 118 N LEU B 105 SHEET 1 AA9 4 VAL B 128 VAL B 133 0 SHEET 2 AA9 4 GLN B 139 SER B 144 -1 O GLY B 143 N THR B 130 SHEET 3 AA9 4 ILE B 149 ASP B 153 -1 O TRP B 152 N ALA B 140 SHEET 4 AA9 4 VAL B 158 TYR B 163 -1 O TYR B 163 N ILE B 149 SHEET 1 AB1 4 VAL B 170 ALA B 175 0 SHEET 2 AB1 4 VAL B 182 SER B 187 -1 O LEU B 184 N ALA B 174 SHEET 3 AB1 4 ILE B 192 ASP B 196 -1 O LEU B 193 N SER B 185 SHEET 4 AB1 4 ALA B 203 ILE B 206 -1 O SER B 204 N LEU B 194 SHEET 1 AB2 4 PRO B 215 TRP B 220 0 SHEET 2 AB2 4 VAL B 227 ASP B 232 -1 O GLY B 231 N THR B 216 SHEET 3 AB2 4 THR B 236 ASP B 241 -1 O VAL B 240 N PHE B 228 SHEET 4 AB2 4 CYS B 247 ALA B 252 -1 O LEU B 249 N LEU B 239 SHEET 1 AB3 4 VAL B 258 PHE B 263 0 SHEET 2 AB3 4 LEU B 271 SER B 275 -1 O ALA B 272 N VAL B 262 SHEET 3 AB3 4 LEU B 280 LEU B 283 -1 O LEU B 283 N LEU B 271 SHEET 4 AB3 4 GLU B 289 SER B 293 -1 O LEU B 290 N VAL B 282 SHEET 1 AB4 3 VAL B 300 TRP B 305 0 SHEET 2 AB4 3 LEU B 312 GLY B 317 -1 O THR B 314 N THR B 304 SHEET 3 AB4 3 VAL B 322 VAL B 326 -1 O HIS B 325 N LEU B 313 SSBOND 1 CYS B 208 CYS B 247 1555 1555 2.03 CISPEP 1 GLU A 57 PRO A 58 0 6.16 CISPEP 2 GLY A 64 PRO A 65 0 0.05 CISPEP 3 ILE A 464 PRO A 465 0 7.88 CISPEP 4 HIS A 523 PRO A 524 0 -0.53 CISPEP 5 ALA A 619 PRO A 620 0 3.45 CISPEP 6 ALA B 67 PRO B 68 0 5.24 SITE 1 AC1 21 LEU A 315 TYR A 324 LYS A 333 TYR A 334 SITE 2 AC1 21 GLY A 365 ALA A 366 GLY A 367 PRO A 370 SITE 3 AC1 21 LEU A 371 GLU A 392 LYS A 393 ASP A 419 SITE 4 AC1 21 MET A 420 ARG A 421 GLU A 435 LEU A 436 SITE 5 AC1 21 CYS A 449 4Z2 A 702 HOH A 806 HOH A 824 SITE 6 AC1 21 HOH A 837 SITE 1 AC2 16 PHE A 300 GLN A 309 PHE A 327 GLU A 435 SITE 2 AC2 16 LEU A 437 GLY A 438 SER A 439 GLU A 444 SITE 3 AC2 16 VAL A 503 PHE A 577 SER A 578 TRP A 579 SITE 4 AC2 16 PHE A 580 SFG A 701 HOH A 822 HOH A 849 SITE 1 AC3 3 PHE A 40 THR A 80 GLN A 263 CRYST1 102.810 137.780 178.910 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009727 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007258 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005589 0.00000