PDB Short entry for 6V2D HEADER GENE REGULATION 22-NOV-19 6V2D TITLE CRYSTAL STRUCTURE OF CHROMODOMAIN OF CDYL2 IN COMPLEX WITH INHIBITOR TITLE 2 UNC3866 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMODOMAIN Y-LIKE PROTEIN 2; COMPND 3 CHAIN: A, C, E, G, I, K; COMPND 4 FRAGMENT: CHROMODOMAIN; COMPND 5 SYNONYM: CDY-LIKE 2, CDYL2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UNC3866; COMPND 9 CHAIN: J, L, B, D, F, H; COMPND 10 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: CDYL2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: -V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, GENE KEYWDS 2 REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,W.TEMPEL,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,J.MIN,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (SGC) REVDAT 4 11-OCT-23 6V2D 1 REMARK REVDAT 3 29-JUL-20 6V2D 1 JRNL REVDAT 2 17-JUN-20 6V2D 1 JRNL REVDAT 1 25-DEC-19 6V2D 0 JRNL AUTH C.DONG,Y.LIU,T.J.LYU,S.BELDAR,K.N.LAMB,W.TEMPEL,Y.LI,Z.LI, JRNL AUTH 2 L.I.JAMES,S.QIN,Y.WANG,J.MIN JRNL TITL STRUCTURAL BASIS FOR THE BINDING SELECTIVITY OF HUMAN CDY JRNL TITL 2 CHROMODOMAINS. JRNL REF CELL CHEM BIOL V. 27 827 2020 JRNL REFN ESSN 2451-9456 JRNL PMID 32470319 JRNL DOI 10.1016/J.CHEMBIOL.2020.05.007 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.250 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 24377 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1203 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.0500 - 4.3700 1.00 3011 151 0.1781 0.2130 REMARK 3 2 4.3700 - 3.4700 0.81 2325 126 0.1746 0.2034 REMARK 3 3 3.4700 - 3.0300 1.00 2843 131 0.2167 0.2702 REMARK 3 4 3.0300 - 2.7500 1.00 2803 158 0.2434 0.3427 REMARK 3 5 2.7500 - 2.5500 1.00 2793 135 0.2478 0.3424 REMARK 3 6 2.5500 - 2.4000 1.00 2767 166 0.2409 0.3127 REMARK 3 7 2.4000 - 2.2800 1.00 2783 162 0.2448 0.3113 REMARK 3 8 2.2800 - 2.1800 0.38 1118 0 0.2715 0.0000 REMARK 3 9 2.1800 - 2.1000 1.00 2731 174 0.2375 0.3073 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.259 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 3409 REMARK 3 ANGLE : 1.050 4606 REMARK 3 CHIRALITY : 0.062 431 REMARK 3 PLANARITY : 0.006 589 REMARK 3 DIHEDRAL : 20.877 1243 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6V2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000241474. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN A200 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28615 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 38.43 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.02300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PRELIMINARY COORDINATES OF PDB ENTRIES 5EPJ AND REMARK 200 5EPK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% P3350, 0.2M AMMONIUM ACETATE, 0.1M REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 22.98950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.64400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.91750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.64400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.98950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.91750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6 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: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 1260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 350 REMARK 350 BIOMOLECULE: 3 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: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 350 REMARK 350 BIOMOLECULE: 4 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: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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 350 REMARK 350 BIOMOLECULE: 5 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: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, J 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 350 REMARK 350 BIOMOLECULE: 6 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: 1250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: K, L 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE UNC3866 IS OLIGOPEPTIDE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: UNC3866 REMARK 400 CHAIN: J, L, B, D, F, H REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 GLY A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 59 REMARK 465 MET A 60 REMARK 465 SER A 61 REMARK 465 LYS A 62 REMARK 465 ASP A 63 REMARK 465 LYS A 64 REMARK 465 GLY C 1 REMARK 465 GLY E 1 REMARK 465 HIS E 59 REMARK 465 MET E 60 REMARK 465 SER E 61 REMARK 465 LYS E 62 REMARK 465 ASP E 63 REMARK 465 LYS E 64 REMARK 465 GLY I 1 REMARK 465 ALA I 2 REMARK 465 SER I 3 REMARK 465 MET I 60 REMARK 465 SER I 61 REMARK 465 LYS I 62 REMARK 465 ASP I 63 REMARK 465 LYS I 64 REMARK 465 GLY K 1 REMARK 465 ALA K 2 REMARK 465 SER K 3 REMARK 465 HIS K 59 REMARK 465 MET K 60 REMARK 465 SER K 61 REMARK 465 LYS K 62 REMARK 465 ASP K 63 REMARK 465 LYS K 64 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 LYS A 19 CE NZ REMARK 470 LYS A 20 CE NZ REMARK 470 LYS A 30 NZ REMARK 470 LEU A 58 C O CB CG CD1 CD2 REMARK 470 ALA C 2 N CB REMARK 470 LYS C 19 CD CE NZ REMARK 470 LYS C 20 CE NZ REMARK 470 LYS C 22 NZ REMARK 470 LYS C 30 NZ REMARK 470 GLU C 54 CD OE1 OE2 REMARK 470 LYS C 62 CE NZ REMARK 470 LYS C 64 CD CE NZ REMARK 470 ALA E 2 N CB REMARK 470 LYS E 19 CG CD CE NZ REMARK 470 LYS E 20 CG CD CE NZ REMARK 470 LYS E 22 CD CE NZ REMARK 470 LYS E 30 NZ REMARK 470 LEU E 58 CG CD1 CD2 REMARK 470 LYS G 19 CG CD CE NZ REMARK 470 LYS G 20 CD CE NZ REMARK 470 LYS G 22 NZ REMARK 470 LYS G 30 NZ REMARK 470 LYS I 17 NZ REMARK 470 LYS I 19 CG CD CE NZ REMARK 470 LYS I 20 CE NZ REMARK 470 LYS I 30 NZ REMARK 470 LYS K 17 CE NZ REMARK 470 LYS K 19 CG CD CE NZ REMARK 470 LYS K 20 CG CD CE NZ REMARK 470 LYS K 22 CD CE NZ REMARK 470 LEU K 58 C O CB CG CD1 CD2 REMARK 470 5R5 L 6 C CB OG O C1 OXT REMARK 470 5R5 B 6 C1 REMARK 470 5R5 H 6 C1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE J 2 CB PHE J 2 CG -0.117 REMARK 500 PHE L 2 CB PHE L 2 CG -0.107 REMARK 500 PHE F 2 CB PHE F 2 CG -0.104 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE L 2 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES 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 UNC3866 chain J REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for UNC3866 chain L REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for UNC3866 chain B REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for UNC3866 chain D REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for UNC3866 chain F REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for UNC3866 chain H DBREF 6V2D A 2 64 UNP Q8N8U2 CDYL2_HUMAN 2 64 DBREF 6V2D C 2 64 UNP Q8N8U2 CDYL2_HUMAN 2 64 DBREF 6V2D E 2 64 UNP Q8N8U2 CDYL2_HUMAN 2 64 DBREF 6V2D G 2 64 UNP Q8N8U2 CDYL2_HUMAN 2 64 DBREF 6V2D I 2 64 UNP Q8N8U2 CDYL2_HUMAN 2 64 DBREF 6V2D K 2 64 UNP Q8N8U2 CDYL2_HUMAN 2 64 DBREF 6V2D J 1 6 PDB 6V2D 6V2D 1 6 DBREF 6V2D L 1 6 PDB 6V2D 6V2D 1 6 DBREF 6V2D B 1 6 PDB 6V2D 6V2D 1 6 DBREF 6V2D D 1 6 PDB 6V2D 6V2D 1 6 DBREF 6V2D F 1 6 PDB 6V2D 6V2D 1 6 DBREF 6V2D H 1 6 PDB 6V2D 6V2D 1 6 SEQADV 6V2D GLY A 1 UNP Q8N8U2 EXPRESSION TAG SEQADV 6V2D GLY C 1 UNP Q8N8U2 EXPRESSION TAG SEQADV 6V2D GLY E 1 UNP Q8N8U2 EXPRESSION TAG SEQADV 6V2D GLY G 1 UNP Q8N8U2 EXPRESSION TAG SEQADV 6V2D GLY I 1 UNP Q8N8U2 EXPRESSION TAG SEQADV 6V2D GLY K 1 UNP Q8N8U2 EXPRESSION TAG SEQRES 1 A 64 GLY ALA SER GLY ASP LEU TYR GLU VAL GLU ARG ILE VAL SEQRES 2 A 64 ASP LYS ARG LYS ASN LYS LYS GLY LYS TRP GLU TYR LEU SEQRES 3 A 64 ILE ARG TRP LYS GLY TYR GLY SER THR GLU ASP THR TRP SEQRES 4 A 64 GLU PRO GLU HIS HIS LEU LEU HIS CYS GLU GLU PHE ILE SEQRES 5 A 64 ASP GLU PHE ASN GLY LEU HIS MET SER LYS ASP LYS SEQRES 1 C 64 GLY ALA SER GLY ASP LEU TYR GLU VAL GLU ARG ILE VAL SEQRES 2 C 64 ASP LYS ARG LYS ASN LYS LYS GLY LYS TRP GLU TYR LEU SEQRES 3 C 64 ILE ARG TRP LYS GLY TYR GLY SER THR GLU ASP THR TRP SEQRES 4 C 64 GLU PRO GLU HIS HIS LEU LEU HIS CYS GLU GLU PHE ILE SEQRES 5 C 64 ASP GLU PHE ASN GLY LEU HIS MET SER LYS ASP LYS SEQRES 1 E 64 GLY ALA SER GLY ASP LEU TYR GLU VAL GLU ARG ILE VAL SEQRES 2 E 64 ASP LYS ARG LYS ASN LYS LYS GLY LYS TRP GLU TYR LEU SEQRES 3 E 64 ILE ARG TRP LYS GLY TYR GLY SER THR GLU ASP THR TRP SEQRES 4 E 64 GLU PRO GLU HIS HIS LEU LEU HIS CYS GLU GLU PHE ILE SEQRES 5 E 64 ASP GLU PHE ASN GLY LEU HIS MET SER LYS ASP LYS SEQRES 1 G 64 GLY ALA SER GLY ASP LEU TYR GLU VAL GLU ARG ILE VAL SEQRES 2 G 64 ASP LYS ARG LYS ASN LYS LYS GLY LYS TRP GLU TYR LEU SEQRES 3 G 64 ILE ARG TRP LYS GLY TYR GLY SER THR GLU ASP THR TRP SEQRES 4 G 64 GLU PRO GLU HIS HIS LEU LEU HIS CYS GLU GLU PHE ILE SEQRES 5 G 64 ASP GLU PHE ASN GLY LEU HIS MET SER LYS ASP LYS SEQRES 1 I 64 GLY ALA SER GLY ASP LEU TYR GLU VAL GLU ARG ILE VAL SEQRES 2 I 64 ASP LYS ARG LYS ASN LYS LYS GLY LYS TRP GLU TYR LEU SEQRES 3 I 64 ILE ARG TRP LYS GLY TYR GLY SER THR GLU ASP THR TRP SEQRES 4 I 64 GLU PRO GLU HIS HIS LEU LEU HIS CYS GLU GLU PHE ILE SEQRES 5 I 64 ASP GLU PHE ASN GLY LEU HIS MET SER LYS ASP LYS SEQRES 1 K 64 GLY ALA SER GLY ASP LEU TYR GLU VAL GLU ARG ILE VAL SEQRES 2 K 64 ASP LYS ARG LYS ASN LYS LYS GLY LYS TRP GLU TYR LEU SEQRES 3 K 64 ILE ARG TRP LYS GLY TYR GLY SER THR GLU ASP THR TRP SEQRES 4 K 64 GLU PRO GLU HIS HIS LEU LEU HIS CYS GLU GLU PHE ILE SEQRES 5 K 64 ASP GLU PHE ASN GLY LEU HIS MET SER LYS ASP LYS SEQRES 1 J 6 5R0 PHE ALA LEU ELY 5R5 SEQRES 1 L 6 5R0 PHE ALA LEU ELY 5R5 SEQRES 1 B 6 5R0 PHE ALA LEU ELY 5R5 SEQRES 1 D 6 5R0 PHE ALA LEU ELY 5R5 SEQRES 1 F 6 5R0 PHE ALA LEU ELY 5R5 SEQRES 1 H 6 5R0 PHE ALA LEU ELY 5R5 HET 5R0 J 1 12 HET ELY J 5 13 HET 5R5 J 6 8 HET 5R0 L 1 12 HET ELY L 5 13 HET 5R5 L 6 2 HET 5R0 B 1 12 HET ELY B 5 13 HET 5R5 B 6 7 HET 5R0 D 1 12 HET ELY D 5 13 HET 5R5 D 6 8 HET 5R0 F 1 12 HET ELY F 5 13 HET 5R5 F 6 8 HET 5R0 H 1 12 HET ELY H 5 13 HET 5R5 H 6 7 HET UNX A 101 1 HET UNX A 102 1 HET UNX A 103 1 HET UNX A 104 1 HET UNX A 105 1 HET UNX A 106 1 HET UNX A 107 1 HET UNX A 108 1 HET UNX C 101 1 HET UNX C 102 1 HET UNX C 103 1 HET UNX C 104 1 HET UNX C 105 1 HET UNX E 101 1 HET UNX G 101 1 HET UNX G 102 1 HET UNX G 103 1 HET UNX G 104 1 HET UNX G 105 1 HET UNX G 106 1 HET UNX I 101 1 HET UNX I 102 1 HET UNX I 103 1 HET UNX I 104 1 HET UNX I 105 1 HET UNX K 101 1 HET UNX K 102 1 HET UNX J 101 1 HETNAM 5R0 4-~{TERT}-BUTYLBENZOIC ACID HETNAM ELY N~6~,N~6~-DIETHYL-L-LYSINE HETNAM 5R5 METHYL L-SERINATE HETNAM UNX UNKNOWN ATOM OR ION HETSYN ELY (2S)-2-AZANYL-6-(DIETHYLAMINO)HEXANOIC ACID HETSYN 5R5 METHYL (2~{S})-2-AZANYL-3-OXIDANYL-PROPANOATE FORMUL 7 5R0 6(C11 H14 O2) FORMUL 7 ELY 6(C10 H22 N2 O2) FORMUL 7 5R5 6(C4 H9 N O3) FORMUL 13 UNX 28(X) FORMUL 41 HOH *150(H2 O) HELIX 1 AA1 GLY A 33 ASP A 37 5 5 HELIX 2 AA2 HIS A 43 LEU A 45 5 3 HELIX 3 AA3 CYS A 48 LEU A 58 1 11 HELIX 4 AA4 GLY C 33 ASP C 37 5 5 HELIX 5 AA5 HIS C 43 LEU C 45 5 3 HELIX 6 AA6 CYS C 48 GLY C 57 1 10 HELIX 7 AA7 GLY E 33 ASP E 37 5 5 HELIX 8 AA8 HIS E 43 LEU E 45 5 3 HELIX 9 AA9 CYS E 48 GLY E 57 1 10 HELIX 10 AB1 GLY G 33 ASP G 37 5 5 HELIX 11 AB2 HIS G 43 LEU G 45 5 3 HELIX 12 AB3 CYS G 48 GLY G 57 1 10 HELIX 13 AB4 LEU G 58 LYS G 64 5 7 HELIX 14 AB5 GLY I 33 ASP I 37 5 5 HELIX 15 AB6 HIS I 43 LEU I 45 5 3 HELIX 16 AB7 CYS I 48 GLY I 57 1 10 HELIX 17 AB8 GLY K 33 ASP K 37 5 5 HELIX 18 AB9 HIS K 43 LEU K 45 5 3 HELIX 19 AC1 CYS K 48 GLY K 57 1 10 SHEET 1 AA1 2 LEU A 6 TYR A 7 0 SHEET 2 AA1 2 ALA B 3 LEU B 4 -1 O ALA B 3 N TYR A 7 SHEET 1 AA2 3 VAL A 9 LYS A 17 0 SHEET 2 AA2 3 TRP A 23 TRP A 29 -1 O LEU A 26 N VAL A 13 SHEET 3 AA2 3 THR A 38 PRO A 41 -1 O GLU A 40 N TYR A 25 SHEET 1 AA3 2 LEU C 6 TYR C 7 0 SHEET 2 AA3 2 ALA D 3 LEU D 4 -1 O ALA D 3 N TYR C 7 SHEET 1 AA4 3 VAL C 9 LYS C 17 0 SHEET 2 AA4 3 TRP C 23 TRP C 29 -1 O GLU C 24 N ARG C 16 SHEET 3 AA4 3 THR C 38 PRO C 41 -1 O THR C 38 N ILE C 27 SHEET 1 AA5 2 LEU E 6 TYR E 7 0 SHEET 2 AA5 2 ALA F 3 LEU F 4 -1 O ALA F 3 N TYR E 7 SHEET 1 AA6 3 VAL E 9 LYS E 17 0 SHEET 2 AA6 3 TRP E 23 TRP E 29 -1 O ARG E 28 N GLU E 10 SHEET 3 AA6 3 THR E 38 PRO E 41 -1 O THR E 38 N ILE E 27 SHEET 1 AA7 2 LEU G 6 TYR G 7 0 SHEET 2 AA7 2 ALA H 3 LEU H 4 -1 O ALA H 3 N TYR G 7 SHEET 1 AA8 3 VAL G 9 LYS G 17 0 SHEET 2 AA8 3 TRP G 23 TRP G 29 -1 O ARG G 28 N GLU G 10 SHEET 3 AA8 3 THR G 38 PRO G 41 -1 O GLU G 40 N TYR G 25 SHEET 1 AA9 2 LEU I 6 TYR I 7 0 SHEET 2 AA9 2 ALA J 3 LEU J 4 -1 O ALA J 3 N TYR I 7 SHEET 1 AB1 3 VAL I 9 LYS I 17 0 SHEET 2 AB1 3 TRP I 23 TRP I 29 -1 O GLU I 24 N ARG I 16 SHEET 3 AB1 3 THR I 38 PRO I 41 -1 O THR I 38 N ILE I 27 SHEET 1 AB2 2 LEU K 6 TYR K 7 0 SHEET 2 AB2 2 ALA L 3 LEU L 4 -1 O ALA L 3 N TYR K 7 SHEET 1 AB3 3 VAL K 9 LYS K 17 0 SHEET 2 AB3 3 TRP K 23 TRP K 29 -1 O LEU K 26 N VAL K 13 SHEET 3 AB3 3 THR K 38 PRO K 41 -1 O GLU K 40 N TYR K 25 LINK C1 5R0 J 1 N PHE J 2 1555 1555 1.34 LINK C LEU J 4 N ELY J 5 1555 1555 1.32 LINK C ELY J 5 N 5R5 J 6 1555 1555 1.33 LINK C1 5R0 L 1 N PHE L 2 1555 1555 1.34 LINK C LEU L 4 N ELY L 5 1555 1555 1.34 LINK C ELY L 5 N 5R5 L 6 1555 1555 1.33 LINK C1 5R0 B 1 N PHE B 2 1555 1555 1.34 LINK C LEU B 4 N ELY B 5 1555 1555 1.33 LINK C ELY B 5 N 5R5 B 6 1555 1555 1.33 LINK C1 5R0 D 1 N PHE D 2 1555 1555 1.34 LINK C LEU D 4 N ELY D 5 1555 1555 1.32 LINK C ELY D 5 N 5R5 D 6 1555 1555 1.32 LINK C1 5R0 F 1 N PHE F 2 1555 1555 1.33 LINK C LEU F 4 N ELY F 5 1555 1555 1.33 LINK C ELY F 5 N 5R5 F 6 1555 1555 1.34 LINK C1 5R0 H 1 N PHE H 2 1555 1555 1.35 LINK C LEU H 4 N ELY H 5 1555 1555 1.32 LINK C ELY H 5 N 5R5 H 6 1555 1555 1.31 SITE 1 AC1 21 ALA C 2 LEU G 6 PHE H 2 ASP I 5 SITE 2 AC1 21 LEU I 6 TYR I 7 GLU I 8 VAL I 9 SITE 3 AC1 21 TRP I 29 TYR I 32 GLU I 40 HIS I 44 SITE 4 AC1 21 LEU I 45 LEU I 46 HIS I 47 CYS I 48 SITE 5 AC1 21 GLU I 50 PHE I 51 HIS K 43 HIS K 44 SITE 6 AC1 21 LEU L 4 SITE 1 AC2 19 SER G 3 HIS G 43 LEU H 4 PHE J 2 SITE 2 AC2 19 ASP K 5 LEU K 6 TYR K 7 GLU K 8 SITE 3 AC2 19 VAL K 9 TRP K 29 TYR K 32 GLU K 40 SITE 4 AC2 19 HIS K 44 LEU K 46 HIS K 47 CYS K 48 SITE 5 AC2 19 GLU K 50 PHE K 51 HOH K 210 SITE 1 AC3 18 ASP A 5 LEU A 6 TYR A 7 GLU A 8 SITE 2 AC3 18 VAL A 9 TRP A 29 TYR A 32 GLU A 40 SITE 3 AC3 18 HIS A 44 LEU A 46 HIS A 47 CYS A 48 SITE 4 AC3 18 PHE A 51 HIS C 43 HIS C 44 HOH C 219 SITE 5 AC3 18 LEU D 4 PHE F 2 SITE 1 AC4 20 PHE B 2 GLY C 4 ASP C 5 LEU C 6 SITE 2 AC4 20 TYR C 7 GLU C 8 VAL C 9 TRP C 29 SITE 3 AC4 20 TYR C 32 GLU C 40 HIS C 44 LEU C 46 SITE 4 AC4 20 HIS C 47 CYS C 48 GLU C 50 PHE C 51 SITE 5 AC4 20 HOH C 211 HIS E 43 HIS E 44 LEU F 4 SITE 1 AC5 18 HIS A 43 LEU B 4 PHE D 2 ASP E 5 SITE 2 AC5 18 LEU E 6 TYR E 7 GLU E 8 VAL E 9 SITE 3 AC5 18 TRP E 29 TYR E 32 GLU E 40 HIS E 44 SITE 4 AC5 18 LEU E 46 HIS E 47 CYS E 48 PHE E 51 SITE 5 AC5 18 HOH E 209 HOH F 101 SITE 1 AC6 18 ASP G 5 LEU G 6 TYR G 7 GLU G 8 SITE 2 AC6 18 VAL G 9 TRP G 29 TYR G 32 GLU G 40 SITE 3 AC6 18 HIS G 44 LEU G 46 HIS G 47 CYS G 48 SITE 4 AC6 18 PHE G 51 HOH G 213 HIS I 43 HIS I 44 SITE 5 AC6 18 LEU J 4 PHE L 2 CRYST1 45.979 83.835 115.288 90.00 90.00 90.00 P 21 21 21 24 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 0.021749 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011928 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008674 0.00000