PDB Short entry for 5V7I HEADER TRANSFERASE/TRANSFERASE INHIBITOR 20-MAR-17 5V7I TITLE CRYSTAL STRUCTURE OF HOMO SAPIENS SERINE HYDROXYMETHYLTRANSFERASE 2 TITLE 2 (MITOCHONDRIAL) (SHMT2), IN COMPLEX WITH GLYCINE, PLP AND FOLATE- TITLE 3 COMPETITIVE PYRAZOLOPYRAN INHIBITOR: 6-AMINO-4-ISOPROPYL-3-METHYL-4- TITLE 4 (3-(PYRROLIDIN-1-YL)-5-(TRIFLUOROMETHYL)PHENYL)-1,4-DIHYDROPYRANO[2, TITLE 5 3-C]PYRAZOLE-5-CARBONITRILE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SHMT,GLYCINE HYDROXYMETHYLTRANSFERASE,SERINE METHYLASE; COMPND 5 EC: 2.1.2.1; COMPND 6 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: SHMT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SHMT2, SERINE CATABOLISM, ANTIFOLATE, TRANSFERASE-TRANSFERASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.S.DUCKER,J.M.GHERGUROVICH,N.MAINOLFI,V.SURI,S.JEONG,A.FRIEDMAN, AUTHOR 2 M.MANFREDI,H.KIM,J.D.RABINOWITZ REVDAT 5 15-NOV-23 5V7I 1 REMARK REVDAT 4 04-OCT-23 5V7I 1 REMARK REVDAT 3 27-NOV-19 5V7I 1 REMARK REVDAT 2 08-NOV-17 5V7I 1 JRNL REVDAT 1 11-OCT-17 5V7I 0 JRNL AUTH G.S.DUCKER,J.M.GHERGUROVICH,N.MAINOLFI,V.SURI,S.K.JEONG, JRNL AUTH 2 S.HSIN-JUNG LI,A.FRIEDMAN,M.G.MANFREDI,Z.GITAI,H.KIM, JRNL AUTH 3 J.D.RABINOWITZ JRNL TITL HUMAN SHMT INHIBITORS REVEAL DEFECTIVE GLYCINE IMPORT AS A JRNL TITL 2 TARGETABLE METABOLIC VULNERABILITY OF DIFFUSE LARGE B-CELL JRNL TITL 3 LYMPHOMA. JRNL REF PROC. NATL. ACAD. SCI. V. 114 11404 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29073064 JRNL DOI 10.1073/PNAS.1706617114 REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 52776 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2775 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) : 2.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3545 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 187 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7246 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 93 REMARK 3 SOLVENT ATOMS : 466 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.32000 REMARK 3 B22 (A**2) : 1.32000 REMARK 3 B33 (A**2) : -4.28000 REMARK 3 B12 (A**2) : 0.66000 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): 0.310 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.232 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.178 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.259 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7517 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7214 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10179 ; 1.238 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16559 ; 0.889 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 928 ; 5.871 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 344 ;34.850 ;22.965 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1256 ;13.184 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 73 ;13.952 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1103 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8515 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1744 ; 0.001 ; 0.020 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): 3712 ; 1.873 ; 5.067 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3708 ; 1.874 ; 5.064 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4640 ; 3.265 ; 7.595 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4639 ; 3.266 ; 7.593 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3804 ; 1.621 ; 5.346 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3804 ; 1.620 ; 5.346 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5540 ; 2.922 ; 7.937 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8712 ; 6.218 ;40.153 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8713 ; 6.218 ;40.157 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 : NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5V7I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57441 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.470 REMARK 200 RESOLUTION RANGE LOW (A) : 83.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.91 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 4PVF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 17% (W/V) PEG REMARK 280 20000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 140.06667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 70.03333 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 105.05000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.01667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 175.08333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 140.06667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 70.03333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 35.01667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 105.05000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 175.08333 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 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 SER A 29 REMARK 465 ASN A 30 REMARK 465 ALA A 31 REMARK 465 ALA A 32 REMARK 465 GLN A 33 REMARK 465 THR A 34 REMARK 465 GLN A 35 REMARK 465 THR A 36 REMARK 465 GLY A 37 REMARK 465 GLU A 38 REMARK 465 ALA A 39 REMARK 465 ASN A 40 REMARK 465 ARG A 41 REMARK 465 GLY A 42 REMARK 465 SER B 29 REMARK 465 ASN B 30 REMARK 465 ALA B 31 REMARK 465 ALA B 32 REMARK 465 GLN B 33 REMARK 465 THR B 34 REMARK 465 GLN B 35 REMARK 465 THR B 36 REMARK 465 GLY B 37 REMARK 465 GLU B 38 REMARK 465 ALA B 39 REMARK 465 ASN B 40 REMARK 465 ARG B 41 REMARK 465 GLY B 42 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 956 O HOH A 956 9555 1.53 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 217 62.76 60.66 REMARK 500 HIS A 279 -147.60 -98.77 REMARK 500 LLP A 280 -132.73 56.22 REMARK 500 ASN A 379 -157.67 -142.69 REMARK 500 ALA A 463 -65.65 -107.09 REMARK 500 SER B 97 53.98 -140.52 REMARK 500 TYR B 176 118.42 -161.62 REMARK 500 ASP B 205 89.99 -69.90 REMARK 500 HIS B 279 -156.88 -92.75 REMARK 500 LLP B 280 -130.42 67.87 REMARK 500 LYS B 297 -61.92 -94.78 REMARK 500 LYS B 461 43.15 -109.32 REMARK 500 ALA B 463 -70.36 -96.77 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 8Z1 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8Z1 B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLY B 603 DBREF 5V7I A 29 504 UNP P34897 GLYM_HUMAN 29 504 DBREF 5V7I B 29 504 UNP P34897 GLYM_HUMAN 29 504 SEQRES 1 A 476 SER ASN ALA ALA GLN THR GLN THR GLY GLU ALA ASN ARG SEQRES 2 A 476 GLY TRP THR GLY GLN GLU SER LEU SER ASP SER ASP PRO SEQRES 3 A 476 GLU MET TRP GLU LEU LEU GLN ARG GLU LYS ASP ARG GLN SEQRES 4 A 476 CYS ARG GLY LEU GLU LEU ILE ALA SER GLU ASN PHE CYS SEQRES 5 A 476 SER ARG ALA ALA LEU GLU ALA LEU GLY SER CYS LEU ASN SEQRES 6 A 476 ASN LYS TYR SER GLU GLY TYR PRO GLY LYS ARG TYR TYR SEQRES 7 A 476 GLY GLY ALA GLU VAL VAL ASP GLU ILE GLU LEU LEU CYS SEQRES 8 A 476 GLN ARG ARG ALA LEU GLU ALA PHE ASP LEU ASP PRO ALA SEQRES 9 A 476 GLN TRP GLY VAL ASN VAL GLN PRO TYR SER GLY SER PRO SEQRES 10 A 476 ALA ASN LEU ALA VAL TYR THR ALA LEU LEU GLN PRO HIS SEQRES 11 A 476 ASP ARG ILE MET GLY LEU ASP LEU PRO ASP GLY GLY HIS SEQRES 12 A 476 LEU THR HIS GLY TYR MET SER ASP VAL LYS ARG ILE SER SEQRES 13 A 476 ALA THR SER ILE PHE PHE GLU SER MET PRO TYR LYS LEU SEQRES 14 A 476 ASN PRO LYS THR GLY LEU ILE ASP TYR ASN GLN LEU ALA SEQRES 15 A 476 LEU THR ALA ARG LEU PHE ARG PRO ARG LEU ILE ILE ALA SEQRES 16 A 476 GLY THR SER ALA TYR ALA ARG LEU ILE ASP TYR ALA ARG SEQRES 17 A 476 MET ARG GLU VAL CYS ASP GLU VAL LYS ALA HIS LEU LEU SEQRES 18 A 476 ALA ASP MET ALA HIS ILE SER GLY LEU VAL ALA ALA LYS SEQRES 19 A 476 VAL ILE PRO SER PRO PHE LYS HIS ALA ASP ILE VAL THR SEQRES 20 A 476 THR THR THR HIS LLP THR LEU ARG GLY ALA ARG SER GLY SEQRES 21 A 476 LEU ILE PHE TYR ARG LYS GLY VAL LYS ALA VAL ASP PRO SEQRES 22 A 476 LYS THR GLY ARG GLU ILE PRO TYR THR PHE GLU ASP ARG SEQRES 23 A 476 ILE ASN PHE ALA VAL PHE PRO SER LEU GLN GLY GLY PRO SEQRES 24 A 476 HIS ASN HIS ALA ILE ALA ALA VAL ALA VAL ALA LEU LYS SEQRES 25 A 476 GLN ALA CYS THR PRO MET PHE ARG GLU TYR SER LEU GLN SEQRES 26 A 476 VAL LEU LYS ASN ALA ARG ALA MET ALA ASP ALA LEU LEU SEQRES 27 A 476 GLU ARG GLY TYR SER LEU VAL SER GLY GLY THR ASP ASN SEQRES 28 A 476 HIS LEU VAL LEU VAL ASP LEU ARG PRO LYS GLY LEU ASP SEQRES 29 A 476 GLY ALA ARG ALA GLU ARG VAL LEU GLU LEU VAL SER ILE SEQRES 30 A 476 THR ALA ASN LYS ASN THR CYS PRO GLY ASP ARG SER ALA SEQRES 31 A 476 ILE THR PRO GLY GLY LEU ARG LEU GLY ALA PRO ALA LEU SEQRES 32 A 476 THR SER ARG GLN PHE ARG GLU ASP ASP PHE ARG ARG VAL SEQRES 33 A 476 VAL ASP PHE ILE ASP GLU GLY VAL ASN ILE GLY LEU GLU SEQRES 34 A 476 VAL LYS SER LYS THR ALA LYS LEU GLN ASP PHE LYS SER SEQRES 35 A 476 PHE LEU LEU LYS ASP SER GLU THR SER GLN ARG LEU ALA SEQRES 36 A 476 ASN LEU ARG GLN ARG VAL GLU GLN PHE ALA ARG ALA PHE SEQRES 37 A 476 PRO MET PRO GLY PHE ASP GLU HIS SEQRES 1 B 476 SER ASN ALA ALA GLN THR GLN THR GLY GLU ALA ASN ARG SEQRES 2 B 476 GLY TRP THR GLY GLN GLU SER LEU SER ASP SER ASP PRO SEQRES 3 B 476 GLU MET TRP GLU LEU LEU GLN ARG GLU LYS ASP ARG GLN SEQRES 4 B 476 CYS ARG GLY LEU GLU LEU ILE ALA SER GLU ASN PHE CYS SEQRES 5 B 476 SER ARG ALA ALA LEU GLU ALA LEU GLY SER CYS LEU ASN SEQRES 6 B 476 ASN LYS TYR SER GLU GLY TYR PRO GLY LYS ARG TYR TYR SEQRES 7 B 476 GLY GLY ALA GLU VAL VAL ASP GLU ILE GLU LEU LEU CYS SEQRES 8 B 476 GLN ARG ARG ALA LEU GLU ALA PHE ASP LEU ASP PRO ALA SEQRES 9 B 476 GLN TRP GLY VAL ASN VAL GLN PRO TYR SER GLY SER PRO SEQRES 10 B 476 ALA ASN LEU ALA VAL TYR THR ALA LEU LEU GLN PRO HIS SEQRES 11 B 476 ASP ARG ILE MET GLY LEU ASP LEU PRO ASP GLY GLY HIS SEQRES 12 B 476 LEU THR HIS GLY TYR MET SER ASP VAL LYS ARG ILE SER SEQRES 13 B 476 ALA THR SER ILE PHE PHE GLU SER MET PRO TYR LYS LEU SEQRES 14 B 476 ASN PRO LYS THR GLY LEU ILE ASP TYR ASN GLN LEU ALA SEQRES 15 B 476 LEU THR ALA ARG LEU PHE ARG PRO ARG LEU ILE ILE ALA SEQRES 16 B 476 GLY THR SER ALA TYR ALA ARG LEU ILE ASP TYR ALA ARG SEQRES 17 B 476 MET ARG GLU VAL CYS ASP GLU VAL LYS ALA HIS LEU LEU SEQRES 18 B 476 ALA ASP MET ALA HIS ILE SER GLY LEU VAL ALA ALA LYS SEQRES 19 B 476 VAL ILE PRO SER PRO PHE LYS HIS ALA ASP ILE VAL THR SEQRES 20 B 476 THR THR THR HIS LLP THR LEU ARG GLY ALA ARG SER GLY SEQRES 21 B 476 LEU ILE PHE TYR ARG LYS GLY VAL LYS ALA VAL ASP PRO SEQRES 22 B 476 LYS THR GLY ARG GLU ILE PRO TYR THR PHE GLU ASP ARG SEQRES 23 B 476 ILE ASN PHE ALA VAL PHE PRO SER LEU GLN GLY GLY PRO SEQRES 24 B 476 HIS ASN HIS ALA ILE ALA ALA VAL ALA VAL ALA LEU LYS SEQRES 25 B 476 GLN ALA CYS THR PRO MET PHE ARG GLU TYR SER LEU GLN SEQRES 26 B 476 VAL LEU LYS ASN ALA ARG ALA MET ALA ASP ALA LEU LEU SEQRES 27 B 476 GLU ARG GLY TYR SER LEU VAL SER GLY GLY THR ASP ASN SEQRES 28 B 476 HIS LEU VAL LEU VAL ASP LEU ARG PRO LYS GLY LEU ASP SEQRES 29 B 476 GLY ALA ARG ALA GLU ARG VAL LEU GLU LEU VAL SER ILE SEQRES 30 B 476 THR ALA ASN LYS ASN THR CYS PRO GLY ASP ARG SER ALA SEQRES 31 B 476 ILE THR PRO GLY GLY LEU ARG LEU GLY ALA PRO ALA LEU SEQRES 32 B 476 THR SER ARG GLN PHE ARG GLU ASP ASP PHE ARG ARG VAL SEQRES 33 B 476 VAL ASP PHE ILE ASP GLU GLY VAL ASN ILE GLY LEU GLU SEQRES 34 B 476 VAL LYS SER LYS THR ALA LYS LEU GLN ASP PHE LYS SER SEQRES 35 B 476 PHE LEU LEU LYS ASP SER GLU THR SER GLN ARG LEU ALA SEQRES 36 B 476 ASN LEU ARG GLN ARG VAL GLU GLN PHE ALA ARG ALA PHE SEQRES 37 B 476 PRO MET PRO GLY PHE ASP GLU HIS MODRES 5V7I LLP A 280 LYS MODIFIED RESIDUE MODRES 5V7I LLP B 280 LYS MODIFIED RESIDUE HET LLP A 280 24 HET LLP B 280 24 HET 8Z1 A 601 31 HET GOL A 602 6 HET PEG A 603 7 HET PEG A 604 7 HET 8Z1 B 601 31 HET GOL B 602 6 HET GLY B 603 5 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM 8Z1 (4R)-6-AMINO-3-METHYL-4-(PROPAN-2-YL)-4-[3-(PYRROLIDIN- HETNAM 2 8Z1 1-YL)-5-(TRIFLUOROMETHYL)PHENYL]-1,4-DIHYDROPYRANO[2, HETNAM 3 8Z1 3-C]PYRAZOLE-5-CARBONITRILE HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM GLY GLYCINE HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 8Z1 2(C22 H24 F3 N5 O) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 5 PEG 2(C4 H10 O3) FORMUL 9 GLY C2 H5 N O2 FORMUL 10 HOH *466(H2 O) HELIX 1 AA1 SER A 48 ASP A 53 1 6 HELIX 2 AA2 ASP A 53 GLY A 70 1 18 HELIX 3 AA3 SER A 81 GLY A 89 1 9 HELIX 4 AA4 SER A 90 LYS A 95 5 6 HELIX 5 AA5 ALA A 109 PHE A 127 1 19 HELIX 6 AA6 SER A 142 LEU A 155 1 14 HELIX 7 AA7 HIS A 171 GLY A 175 5 5 HELIX 8 AA8 SER A 184 PHE A 190 1 7 HELIX 9 AA9 ASP A 205 ARG A 217 1 13 HELIX 10 AB1 ASP A 233 LYS A 245 1 13 HELIX 11 AB2 ILE A 255 ALA A 261 1 7 HELIX 12 AB3 SER A 266 HIS A 270 5 5 HELIX 13 AB4 HIS A 279 ARG A 283 5 5 HELIX 14 AB5 PHE A 311 PHE A 320 1 10 HELIX 15 AB6 HIS A 328 ALA A 342 1 15 HELIX 16 AB7 THR A 344 ARG A 368 1 25 HELIX 17 AB8 SER A 374 GLY A 376 5 3 HELIX 18 AB9 ARG A 387 GLY A 390 5 4 HELIX 19 AC1 ASP A 392 VAL A 403 1 12 HELIX 20 AC2 ALA A 428 ARG A 434 1 7 HELIX 21 AC3 ARG A 437 LYS A 461 1 25 HELIX 22 AC4 LYS A 464 ASP A 475 1 12 HELIX 23 AC5 ASP A 475 ALA A 495 1 21 HELIX 24 AC6 SER B 48 ASP B 53 1 6 HELIX 25 AC7 ASP B 53 GLY B 70 1 18 HELIX 26 AC8 SER B 81 GLY B 89 1 9 HELIX 27 AC9 SER B 90 LYS B 95 5 6 HELIX 28 AD1 ALA B 109 PHE B 127 1 19 HELIX 29 AD2 SER B 142 LEU B 155 1 14 HELIX 30 AD3 HIS B 171 GLY B 175 5 5 HELIX 31 AD4 SER B 184 PHE B 190 1 7 HELIX 32 AD5 ASP B 205 ARG B 217 1 13 HELIX 33 AD6 ASP B 233 VAL B 244 1 12 HELIX 34 AD7 ILE B 255 ALA B 261 1 7 HELIX 35 AD8 SER B 266 HIS B 270 5 5 HELIX 36 AD9 HIS B 279 ARG B 283 5 5 HELIX 37 AE1 THR B 310 PHE B 320 1 11 HELIX 38 AE2 HIS B 328 CYS B 343 1 16 HELIX 39 AE3 THR B 344 GLU B 367 1 24 HELIX 40 AE4 SER B 374 GLY B 376 5 3 HELIX 41 AE5 ARG B 387 GLY B 390 5 4 HELIX 42 AE6 ASP B 392 VAL B 403 1 12 HELIX 43 AE7 ALA B 428 ARG B 434 1 7 HELIX 44 AE8 ARG B 437 LYS B 461 1 25 HELIX 45 AE9 LYS B 464 ASP B 475 1 12 HELIX 46 AF1 ASP B 475 ALA B 495 1 21 SHEET 1 AA1 2 LEU A 71 GLU A 72 0 SHEET 2 AA1 2 ILE A 405 THR A 406 1 O THR A 406 N LEU A 71 SHEET 1 AA2 2 GLY A 99 TYR A 100 0 SHEET 2 AA2 2 LYS A 103 ARG A 104 -1 O LYS A 103 N TYR A 100 SHEET 1 AA3 7 TRP A 134 ASN A 137 0 SHEET 2 AA3 7 GLY A 288 ARG A 293 -1 O ILE A 290 N ASN A 137 SHEET 3 AA3 7 ILE A 273 THR A 277 -1 N VAL A 274 O PHE A 291 SHEET 4 AA3 7 HIS A 247 ASP A 251 1 N ALA A 250 O ILE A 273 SHEET 5 AA3 7 LEU A 220 ALA A 223 1 N ALA A 223 O LEU A 249 SHEET 6 AA3 7 ARG A 160 LEU A 164 1 N MET A 162 O ILE A 222 SHEET 7 AA3 7 GLU A 191 TYR A 195 1 O GLU A 191 N ILE A 161 SHEET 1 AA4 2 VAL A 296 VAL A 299 0 SHEET 2 AA4 2 GLU A 306 PRO A 308 -1 O ILE A 307 N LYS A 297 SHEET 1 AA5 4 SER A 371 LEU A 372 0 SHEET 2 AA5 4 LEU A 381 ASP A 385 -1 O ASP A 385 N SER A 371 SHEET 3 AA5 4 GLY A 423 GLY A 427 -1 O LEU A 424 N VAL A 384 SHEET 4 AA5 4 ASN A 408 ASN A 410 -1 N ASN A 408 O ARG A 425 SHEET 1 AA6 2 LEU B 71 GLU B 72 0 SHEET 2 AA6 2 ILE B 405 THR B 406 1 O THR B 406 N LEU B 71 SHEET 1 AA7 2 GLY B 99 TYR B 100 0 SHEET 2 AA7 2 LYS B 103 ARG B 104 -1 O LYS B 103 N TYR B 100 SHEET 1 AA8 7 TRP B 134 ASN B 137 0 SHEET 2 AA8 7 GLY B 288 ARG B 293 -1 O ILE B 290 N ASN B 137 SHEET 3 AA8 7 ILE B 273 THR B 277 -1 N VAL B 274 O PHE B 291 SHEET 4 AA8 7 HIS B 247 ASP B 251 1 N ALA B 250 O ILE B 273 SHEET 5 AA8 7 LEU B 220 GLY B 224 1 N ALA B 223 O LEU B 249 SHEET 6 AA8 7 ARG B 160 LEU B 164 1 N MET B 162 O ILE B 222 SHEET 7 AA8 7 GLU B 191 TYR B 195 1 O GLU B 191 N ILE B 161 SHEET 1 AA9 2 VAL B 296 ASP B 300 0 SHEET 2 AA9 2 ARG B 305 PRO B 308 -1 O ILE B 307 N ALA B 298 SHEET 1 AB1 4 SER B 371 LEU B 372 0 SHEET 2 AB1 4 LEU B 381 ASP B 385 -1 O ASP B 385 N SER B 371 SHEET 3 AB1 4 GLY B 423 GLY B 427 -1 O LEU B 424 N VAL B 384 SHEET 4 AB1 4 ASN B 408 LYS B 409 -1 N ASN B 408 O ARG B 425 LINK C HIS A 279 N LLP A 280 1555 1555 1.33 LINK C LLP A 280 N THR A 281 1555 1555 1.33 LINK C HIS B 279 N LLP B 280 1555 1555 1.34 LINK C LLP B 280 N THR B 281 1555 1555 1.34 CISPEP 1 PHE A 320 PRO A 321 0 17.24 CISPEP 2 PHE B 320 PRO B 321 0 14.91 SITE 1 AC1 8 LEU A 166 GLY A 170 HIS A 171 LEU A 172 SITE 2 AC1 8 SER A 226 LYS A 409 TYR B 105 TYR B 106 SITE 1 AC2 5 LYS A 200 VAL A 373 SER A 374 GLY A 375 SITE 2 AC2 5 HOH A 716 SITE 1 AC3 5 ASP A 128 GLN A 133 TRP A 134 LYS A 269 SITE 2 AC3 5 ARG A 293 SITE 1 AC4 2 ARG A 217 HOH A 776 SITE 1 AC5 10 GLU A 98 TYR A 105 TYR A 106 LEU B 166 SITE 2 AC5 10 GLY B 170 HIS B 171 LEU B 172 SER B 226 SITE 3 AC5 10 LYS B 409 GLY B 603 SITE 1 AC6 5 ARG B 387 SER B 417 THR B 420 GLY B 422 SITE 2 AC6 5 HOH B 733 SITE 1 AC7 10 TYR A 96 GLU A 98 TYR A 106 SER B 76 SITE 2 AC7 10 SER B 226 HIS B 254 LLP B 280 ARG B 425 SITE 3 AC7 10 8Z1 B 601 HOH B 730 CRYST1 160.140 160.140 210.100 90.00 90.00 120.00 P 65 2 2 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 0.006245 0.003605 0.000000 0.00000 SCALE2 0.000000 0.007211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004760 0.00000