HEADER TRANSLATION 09-JUN-22 7Y28 TITLE CONTROLLING FIBROSIS USING COMPOUND WITH NOVEL BINDING MODE TO PROLYL- TITLE 2 TRNA SYNTHETASE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE,CELL PROLIFERATION- COMPND 5 INDUCING GENE 32 PROTEIN,GLUTAMATYL-PROLYL-TRNA SYNTHETASE; COMPND 6 EC: 6.1.1.17,6.1.1.15; COMPND 7 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: EPRS1, EPRS, GLNS, PARS, QARS, QPRS, PIG32; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROLYL-TRNA SYNTHETASE, INHIBITOR, FIBROSIS, BINDING MODE, KEYWDS 2 TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR S.KIM,I.YOON,J.SON,S.PARK,K.Y.HWANG REVDAT 3 29-NOV-23 7Y28 1 REMARK REVDAT 2 20-SEP-23 7Y28 1 JRNL REVDAT 1 05-JUL-23 7Y28 0 JRNL AUTH I.YOON,S.KIM,M.CHO,K.A.YOU,J.SON,C.LEE,J.H.SUH,D.J.BAE, JRNL AUTH 2 J.M.KIM,S.OH,S.PARK,S.KIM,S.H.CHO,S.PARK,K.BANG,M.SEO, JRNL AUTH 3 J.H.KIM,B.LEE,J.S.PARK,K.Y.HWANG,S.KIM JRNL TITL CONTROL OF FIBROSIS WITH ENHANCED SAFETY VIA ASYMMETRIC JRNL TITL 2 INHIBITION OF PROLYL-TRNA SYNTHETASE 1. JRNL REF EMBO MOL MED V. 15 16940 2023 JRNL REFN ESSN 1757-4684 JRNL PMID 37212275 JRNL DOI 10.15252/EMMM.202216940 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4438 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.530 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 45110 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.430 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 45.4300 - 5.5100 0.99 3329 154 0.1904 0.2354 REMARK 3 2 5.5100 - 4.3700 1.00 3310 153 0.1586 0.2143 REMARK 3 3 4.3700 - 3.8200 1.00 3272 153 0.1612 0.2103 REMARK 3 4 3.8200 - 3.4700 1.00 3279 151 0.1873 0.2666 REMARK 3 5 3.4700 - 3.2200 0.99 3239 151 0.2022 0.2490 REMARK 3 6 3.2200 - 3.0300 0.98 3221 149 0.2209 0.3321 REMARK 3 7 3.0300 - 2.8800 0.96 3135 145 0.2459 0.2987 REMARK 3 8 2.8800 - 2.7600 0.95 3125 146 0.2402 0.2685 REMARK 3 9 2.7600 - 2.6500 0.95 3087 143 0.2510 0.3091 REMARK 3 10 2.6500 - 2.5600 0.94 3058 143 0.2588 0.2901 REMARK 3 11 2.5600 - 2.4800 0.91 2997 138 0.2793 0.3463 REMARK 3 12 2.4800 - 2.4100 0.89 2941 136 0.2990 0.3503 REMARK 3 13 2.4100 - 2.3400 0.84 2716 127 0.3216 0.3814 REMARK 3 14 2.3400 - 2.2900 0.74 2401 111 0.3288 0.3758 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.02 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7Y28 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030132. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45110 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 45.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 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 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: PHENIX REMARK 200 STARTING MODEL: 4K88 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3500, CACL2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 46.19000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 6960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 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 GLY A 1310 REMARK 465 ILE A 1311 REMARK 465 THR A 1312 REMARK 465 ASN A 1313 REMARK 465 ASP A 1464 REMARK 465 GLN A 1465 REMARK 465 ASP A 1466 REMARK 465 LEU A 1467 REMARK 465 GLU A 1468 REMARK 465 PRO A 1469 REMARK 465 GLY A 1470 REMARK 465 ALA A 1471 REMARK 465 PRO A 1472 REMARK 465 SER A 1473 REMARK 465 MET A 1474 REMARK 465 GLY A 1498 REMARK 465 LYS A 1499 REMARK 465 ILE B 1311 REMARK 465 THR B 1312 REMARK 465 ASN B 1313 REMARK 465 ALA B 1314 REMARK 465 LEU B 1315 REMARK 465 SER B 1316 REMARK 465 GLU B 1317 REMARK 465 ARG B 1463 REMARK 465 ASP B 1464 REMARK 465 GLN B 1465 REMARK 465 ASP B 1466 REMARK 465 LEU B 1467 REMARK 465 GLU B 1468 REMARK 465 PRO B 1469 REMARK 465 GLY B 1470 REMARK 465 ALA B 1471 REMARK 465 PRO B 1472 REMARK 465 SER B 1473 REMARK 465 MET B 1474 REMARK 465 GLN B 1490 REMARK 465 PRO B 1491 REMARK 465 GLY B 1492 REMARK 465 ALA B 1493 REMARK 465 LYS B 1494 REMARK 465 CYS B 1495 REMARK 465 VAL B 1496 REMARK 465 CYS B 1497 REMARK 465 GLY B 1498 REMARK 465 LYS B 1499 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 B1091 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ARG A 1463 O HOH A 2701 2.00 REMARK 500 N ALA A 1314 O HOH A 2702 2.05 REMARK 500 O ALA B 1300 NH1 ARG B 1340 2.07 REMARK 500 O ARG B 1332 N SER B 1336 2.11 REMARK 500 O GLU B 1036 O HOH B 2701 2.13 REMARK 500 OE1 GLN B 1188 O HOH B 2702 2.13 REMARK 500 OE2 GLU B 1264 O HOH B 2703 2.14 REMARK 500 OG SER A 1230 OD2 ASP A 1419 2.15 REMARK 500 OE1 GLN A 1246 O HOH A 2703 2.15 REMARK 500 OE2 GLU B 1450 O HOH B 2704 2.16 REMARK 500 O GLU A 1090 O HOH A 2704 2.16 REMARK 500 OG SER A 1232 OH TYR A 1512 2.18 REMARK 500 OG SER B 1439 NZ LYS B 1441 2.18 REMARK 500 N GLY B 1475 O HOH B 2705 2.19 REMARK 500 ND2 ASN A 1023 OD1 ASP A 1026 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 PRO B1485 CG PRO B1485 CD -0.248 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 A1161 C - N - CA ANGL. DEV. = 20.6 DEGREES REMARK 500 PRO A1491 C - N - CD ANGL. DEV. = -24.9 DEGREES REMARK 500 LEU B1087 CB - CG - CD1 ANGL. DEV. = -13.2 DEGREES REMARK 500 ALA B1095 C - N - CA ANGL. DEV. = -17.6 DEGREES REMARK 500 ASP B1096 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B1096 CB - CG - OD2 ANGL. DEV. = -9.8 DEGREES REMARK 500 PHE B1161 C - N - CA ANGL. DEV. = 20.4 DEGREES REMARK 500 PHE B1161 CB - CA - C ANGL. DEV. = -12.0 DEGREES REMARK 500 CYS B1453 CA - CB - SG ANGL. DEV. = 10.3 DEGREES REMARK 500 PRO B1485 CA - N - CD ANGL. DEV. = -12.3 DEGREES REMARK 500 PRO B1485 CA - CB - CG ANGL. DEV. = -13.2 DEGREES REMARK 500 LEU B1486 N - CA - CB ANGL. DEV. = -12.4 DEGREES REMARK 500 LEU B1486 CA - CB - CG ANGL. DEV. = 19.5 DEGREES REMARK 500 LEU B1486 CB - CG - CD1 ANGL. DEV. = -23.1 DEGREES REMARK 500 CYS B1487 CA - CB - SG ANGL. DEV. = 9.0 DEGREES 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 GLU A1036 30.30 71.52 REMARK 500 PHE A1161 -15.75 69.95 REMARK 500 GLN A1490 -102.98 84.97 REMARK 500 PRO A1491 76.40 19.11 REMARK 500 PHE B1161 -17.30 69.29 REMARK 500 ARG B1331 -127.09 34.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 1315 SER A 1316 -138.74 REMARK 500 GLN A 1490 PRO A 1491 -122.98 REMARK 500 GLU B 1088 LYS B 1089 -138.00 REMARK 500 TYR B 1330 ARG B 1331 139.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A2605 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A1237 OE1 REMARK 620 2 ATP A2602 O2G 81.2 REMARK 620 3 ATP A2602 O1B 89.7 88.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1448 SG REMARK 620 2 CYS A1453 SG 137.1 REMARK 620 3 CYS A1495 SG 96.9 125.3 REMARK 620 4 CYS A1497 SG 88.3 88.6 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A2604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A2602 O1G REMARK 620 2 ATP A2602 O2B 81.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1448 SG REMARK 620 2 CYS B1453 SG 81.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B2604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP B2602 O3G REMARK 620 2 ATP B2602 O1B 67.6 REMARK 620 N 1 DBREF 7Y28 A 1016 1512 UNP P07814 SYEP_HUMAN 1016 1512 DBREF 7Y28 B 1016 1512 UNP P07814 SYEP_HUMAN 1016 1512 SEQRES 1 A 497 LEU GLU ALA LYS LYS GLU GLU ASN LEU ALA ASP TRP TYR SEQRES 2 A 497 SER GLN VAL ILE THR LYS SER GLU MET ILE GLU TYR HIS SEQRES 3 A 497 ASP ILE SER GLY CYS TYR ILE LEU ARG PRO TRP ALA TYR SEQRES 4 A 497 ALA ILE TRP GLU ALA ILE LYS ASP PHE PHE ASP ALA GLU SEQRES 5 A 497 ILE LYS LYS LEU GLY VAL GLU ASN CYS TYR PHE PRO MET SEQRES 6 A 497 PHE VAL SER GLN SER ALA LEU GLU LYS GLU LYS THR HIS SEQRES 7 A 497 VAL ALA ASP PHE ALA PRO GLU VAL ALA TRP VAL THR ARG SEQRES 8 A 497 SER GLY LYS THR GLU LEU ALA GLU PRO ILE ALA ILE ARG SEQRES 9 A 497 PRO THR SER GLU THR VAL MET TYR PRO ALA TYR ALA LYS SEQRES 10 A 497 TRP VAL GLN SER HIS ARG ASP LEU PRO ILE LYS LEU ASN SEQRES 11 A 497 GLN TRP CYS ASN VAL VAL ARG TRP GLU PHE LYS HIS PRO SEQRES 12 A 497 GLN PRO PHE LEU ARG THR ARG GLU PHE LEU TRP GLN GLU SEQRES 13 A 497 GLY HIS SER ALA PHE ALA THR MET GLU GLU ALA ALA GLU SEQRES 14 A 497 GLU VAL LEU GLN ILE LEU ASP LEU TYR ALA GLN VAL TYR SEQRES 15 A 497 GLU GLU LEU LEU ALA ILE PRO VAL VAL LYS GLY ARG LYS SEQRES 16 A 497 THR GLU LYS GLU LYS PHE ALA GLY GLY ASP TYR THR THR SEQRES 17 A 497 THR ILE GLU ALA PHE ILE SER ALA SER GLY ARG ALA ILE SEQRES 18 A 497 GLN GLY GLY THR SER HIS HIS LEU GLY GLN ASN PHE SER SEQRES 19 A 497 LYS MET PHE GLU ILE VAL PHE GLU ASP PRO LYS ILE PRO SEQRES 20 A 497 GLY GLU LYS GLN PHE ALA TYR GLN ASN SER TRP GLY LEU SEQRES 21 A 497 THR THR ARG THR ILE GLY VAL MET THR MET VAL HIS GLY SEQRES 22 A 497 ASP ASN MET GLY LEU VAL LEU PRO PRO ARG VAL ALA CYS SEQRES 23 A 497 VAL GLN VAL VAL ILE ILE PRO CYS GLY ILE THR ASN ALA SEQRES 24 A 497 LEU SER GLU GLU ASP LYS GLU ALA LEU ILE ALA LYS CYS SEQRES 25 A 497 ASN ASP TYR ARG ARG ARG LEU LEU SER VAL ASN ILE ARG SEQRES 26 A 497 VAL ARG ALA ASP LEU ARG ASP ASN TYR SER PRO GLY TRP SEQRES 27 A 497 LYS PHE ASN HIS TRP GLU LEU LYS GLY VAL PRO ILE ARG SEQRES 28 A 497 LEU GLU VAL GLY PRO ARG ASP MET LYS SER CYS GLN PHE SEQRES 29 A 497 VAL ALA VAL ARG ARG ASP THR GLY GLU LYS LEU THR VAL SEQRES 30 A 497 ALA GLU ASN GLU ALA GLU THR LYS LEU GLN ALA ILE LEU SEQRES 31 A 497 GLU ASP ILE GLN VAL THR LEU PHE THR ARG ALA SER GLU SEQRES 32 A 497 ASP LEU LYS THR HIS MET VAL VAL ALA ASN THR MET GLU SEQRES 33 A 497 ASP PHE GLN LYS ILE LEU ASP SER GLY LYS ILE VAL GLN SEQRES 34 A 497 ILE PRO PHE CYS GLY GLU ILE ASP CYS GLU ASP TRP ILE SEQRES 35 A 497 LYS LYS THR THR ALA ARG ASP GLN ASP LEU GLU PRO GLY SEQRES 36 A 497 ALA PRO SER MET GLY ALA LYS SER LEU CYS ILE PRO PHE SEQRES 37 A 497 LYS PRO LEU CYS GLU LEU GLN PRO GLY ALA LYS CYS VAL SEQRES 38 A 497 CYS GLY LYS ASN PRO ALA LYS TYR TYR THR LEU PHE GLY SEQRES 39 A 497 ARG SER TYR SEQRES 1 B 497 LEU GLU ALA LYS LYS GLU GLU ASN LEU ALA ASP TRP TYR SEQRES 2 B 497 SER GLN VAL ILE THR LYS SER GLU MET ILE GLU TYR HIS SEQRES 3 B 497 ASP ILE SER GLY CYS TYR ILE LEU ARG PRO TRP ALA TYR SEQRES 4 B 497 ALA ILE TRP GLU ALA ILE LYS ASP PHE PHE ASP ALA GLU SEQRES 5 B 497 ILE LYS LYS LEU GLY VAL GLU ASN CYS TYR PHE PRO MET SEQRES 6 B 497 PHE VAL SER GLN SER ALA LEU GLU LYS GLU LYS THR HIS SEQRES 7 B 497 VAL ALA ASP PHE ALA PRO GLU VAL ALA TRP VAL THR ARG SEQRES 8 B 497 SER GLY LYS THR GLU LEU ALA GLU PRO ILE ALA ILE ARG SEQRES 9 B 497 PRO THR SER GLU THR VAL MET TYR PRO ALA TYR ALA LYS SEQRES 10 B 497 TRP VAL GLN SER HIS ARG ASP LEU PRO ILE LYS LEU ASN SEQRES 11 B 497 GLN TRP CYS ASN VAL VAL ARG TRP GLU PHE LYS HIS PRO SEQRES 12 B 497 GLN PRO PHE LEU ARG THR ARG GLU PHE LEU TRP GLN GLU SEQRES 13 B 497 GLY HIS SER ALA PHE ALA THR MET GLU GLU ALA ALA GLU SEQRES 14 B 497 GLU VAL LEU GLN ILE LEU ASP LEU TYR ALA GLN VAL TYR SEQRES 15 B 497 GLU GLU LEU LEU ALA ILE PRO VAL VAL LYS GLY ARG LYS SEQRES 16 B 497 THR GLU LYS GLU LYS PHE ALA GLY GLY ASP TYR THR THR SEQRES 17 B 497 THR ILE GLU ALA PHE ILE SER ALA SER GLY ARG ALA ILE SEQRES 18 B 497 GLN GLY GLY THR SER HIS HIS LEU GLY GLN ASN PHE SER SEQRES 19 B 497 LYS MET PHE GLU ILE VAL PHE GLU ASP PRO LYS ILE PRO SEQRES 20 B 497 GLY GLU LYS GLN PHE ALA TYR GLN ASN SER TRP GLY LEU SEQRES 21 B 497 THR THR ARG THR ILE GLY VAL MET THR MET VAL HIS GLY SEQRES 22 B 497 ASP ASN MET GLY LEU VAL LEU PRO PRO ARG VAL ALA CYS SEQRES 23 B 497 VAL GLN VAL VAL ILE ILE PRO CYS GLY ILE THR ASN ALA SEQRES 24 B 497 LEU SER GLU GLU ASP LYS GLU ALA LEU ILE ALA LYS CYS SEQRES 25 B 497 ASN ASP TYR ARG ARG ARG LEU LEU SER VAL ASN ILE ARG SEQRES 26 B 497 VAL ARG ALA ASP LEU ARG ASP ASN TYR SER PRO GLY TRP SEQRES 27 B 497 LYS PHE ASN HIS TRP GLU LEU LYS GLY VAL PRO ILE ARG SEQRES 28 B 497 LEU GLU VAL GLY PRO ARG ASP MET LYS SER CYS GLN PHE SEQRES 29 B 497 VAL ALA VAL ARG ARG ASP THR GLY GLU LYS LEU THR VAL SEQRES 30 B 497 ALA GLU ASN GLU ALA GLU THR LYS LEU GLN ALA ILE LEU SEQRES 31 B 497 GLU ASP ILE GLN VAL THR LEU PHE THR ARG ALA SER GLU SEQRES 32 B 497 ASP LEU LYS THR HIS MET VAL VAL ALA ASN THR MET GLU SEQRES 33 B 497 ASP PHE GLN LYS ILE LEU ASP SER GLY LYS ILE VAL GLN SEQRES 34 B 497 ILE PRO PHE CYS GLY GLU ILE ASP CYS GLU ASP TRP ILE SEQRES 35 B 497 LYS LYS THR THR ALA ARG ASP GLN ASP LEU GLU PRO GLY SEQRES 36 B 497 ALA PRO SER MET GLY ALA LYS SER LEU CYS ILE PRO PHE SEQRES 37 B 497 LYS PRO LEU CYS GLU LEU GLN PRO GLY ALA LYS CYS VAL SEQRES 38 B 497 CYS GLY LYS ASN PRO ALA LYS TYR TYR THR LEU PHE GLY SEQRES 39 B 497 ARG SER TYR HET F96 A2601 27 HET ATP A2602 31 HET ZN A2603 1 HET MG A2604 1 HET MG A2605 1 HET F96 B2601 27 HET ATP B2602 31 HET ZN B2603 1 HET MG B2604 1 HET MG B2605 1 HETNAM F96 1-[6-(3-FLUOROPHENYL)BENZIMIDAZOL-1-YL]-3-[(2R,3S)-3- HETNAM 2 F96 OXIDANYLPIPERIDIN-2-YL]PROPAN-2-ONE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 3 F96 2(C21 H22 F N3 O2) FORMUL 4 ATP 2(C10 H16 N5 O13 P3) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 MG 4(MG 2+) FORMUL 13 HOH *132(H2 O) HELIX 1 AA1 ASN A 1023 SER A 1035 1 13 HELIX 2 AA2 ARG A 1050 LEU A 1071 1 22 HELIX 3 AA3 GLN A 1084 GLU A 1090 1 7 HELIX 4 AA4 VAL A 1094 GLU A 1100 5 7 HELIX 5 AA5 SER A 1122 VAL A 1134 1 13 HELIX 6 AA6 SER A 1136 LEU A 1140 5 5 HELIX 7 AA7 THR A 1178 LEU A 1200 1 23 HELIX 8 AA8 GLN A 1246 GLU A 1253 1 8 HELIX 9 AA9 THR A 1277 GLY A 1288 1 12 HELIX 10 AB1 SER A 1316 VAL A 1337 1 22 HELIX 11 AB2 SER A 1350 LYS A 1361 1 12 HELIX 12 AB3 GLY A 1370 SER A 1376 1 7 HELIX 13 AB4 GLU A 1396 HIS A 1423 1 28 HELIX 14 AB5 THR A 1429 SER A 1439 1 11 HELIX 15 AB6 GLU A 1450 THR A 1461 1 12 HELIX 16 AB7 ASN B 1023 SER B 1035 1 13 HELIX 17 AB8 ARG B 1050 LEU B 1071 1 22 HELIX 18 AB9 GLN B 1084 LYS B 1089 1 6 HELIX 19 AC1 PHE B 1097 GLU B 1100 5 4 HELIX 20 AC2 SER B 1122 VAL B 1134 1 13 HELIX 21 AC3 SER B 1136 LEU B 1140 5 5 HELIX 22 AC4 THR B 1178 LEU B 1200 1 23 HELIX 23 AC5 GLN B 1246 GLU B 1253 1 8 HELIX 24 AC6 THR B 1277 GLY B 1288 1 12 HELIX 25 AC7 LYS B 1320 SER B 1336 1 17 HELIX 26 AC8 SER B 1350 GLY B 1362 1 13 HELIX 27 AC9 GLY B 1370 SER B 1376 1 7 HELIX 28 AD1 GLU B 1396 HIS B 1423 1 28 HELIX 29 AD2 THR B 1429 ASP B 1438 1 10 HELIX 30 AD3 GLU B 1450 THR B 1461 1 12 SHEET 1 AA1 2 ILE A1038 TYR A1040 0 SHEET 2 AA1 2 TYR A1047 LEU A1049 -1 O ILE A1048 N GLU A1039 SHEET 1 AA211 GLU A1074 ASN A1075 0 SHEET 2 AA211 ILE A1142 VAL A1151 1 O ASN A1145 N GLU A1074 SHEET 3 AA211 GLU A1166 PHE A1176 -1 O HIS A1173 N LEU A1144 SHEET 4 AA211 TYR A1269 THR A1276 -1 O TYR A1269 N PHE A1176 SHEET 5 AA211 ARG A1234 GLY A1245 -1 N HIS A1242 O SER A1272 SHEET 6 AA211 TYR A1221 ILE A1229 -1 N ILE A1229 O ARG A1234 SHEET 7 AA211 VAL A1206 ARG A1209 -1 N GLY A1208 O THR A1224 SHEET 8 AA211 LYS A1477 PRO A1482 -1 O ILE A1481 N ARG A1209 SHEET 9 AA211 TYR A1504 GLY A1509 -1 O LEU A1507 N LEU A1479 SHEET 10 AA211 ILE A1442 PHE A1447 -1 N VAL A1443 O PHE A1508 SHEET 11 AA211 MET A1424 VAL A1426 1 N VAL A1425 O GLN A1444 SHEET 1 AA3 6 PHE A1081 SER A1083 0 SHEET 2 AA3 6 THR A1110 ILE A1118 -1 O ALA A1117 N VAL A1082 SHEET 3 AA3 6 ALA A1102 SER A1107 -1 N VAL A1104 O ILE A1116 SHEET 4 AA3 6 ALA B1102 SER B1107 -1 O ARG B1106 N TRP A1103 SHEET 5 AA3 6 THR B1110 ILE B1118 -1 O ILE B1116 N VAL B1104 SHEET 6 AA3 6 PHE B1081 SER B1083 -1 N VAL B1082 O ALA B1117 SHEET 1 AA4 2 VAL A1255 GLU A1257 0 SHEET 2 AA4 2 LYS A1265 PHE A1267 -1 O GLN A1266 N PHE A1256 SHEET 1 AA5 5 VAL A1341 ALA A1343 0 SHEET 2 AA5 5 VAL A1304 PRO A1308 1 N ILE A1306 O ARG A1342 SHEET 3 AA5 5 ILE A1365 VAL A1369 1 O LEU A1367 N VAL A1305 SHEET 4 AA5 5 GLN A1378 ARG A1383 -1 O VAL A1380 N GLU A1368 SHEET 5 AA5 5 LYS A1389 ALA A1393 -1 O LEU A1390 N ALA A1381 SHEET 1 AA6 2 ILE B1038 TYR B1040 0 SHEET 2 AA6 2 TYR B1047 LEU B1049 -1 O ILE B1048 N GLU B1039 SHEET 1 AA711 GLU B1074 ASN B1075 0 SHEET 2 AA711 ILE B1142 VAL B1151 1 O ASN B1145 N GLU B1074 SHEET 3 AA711 GLU B1166 PHE B1176 -1 O HIS B1173 N LEU B1144 SHEET 4 AA711 TYR B1269 THR B1276 -1 O TYR B1269 N PHE B1176 SHEET 5 AA711 ARG B1234 GLY B1245 -1 N LEU B1244 O GLN B1270 SHEET 6 AA711 TYR B1221 ILE B1229 -1 N ILE B1225 O GLY B1238 SHEET 7 AA711 VAL B1206 ARG B1209 -1 N GLY B1208 O THR B1224 SHEET 8 AA711 LYS B1477 PRO B1482 -1 O ILE B1481 N ARG B1209 SHEET 9 AA711 TYR B1504 GLY B1509 -1 O GLY B1509 N LYS B1477 SHEET 10 AA711 ILE B1442 PHE B1447 -1 N VAL B1443 O PHE B1508 SHEET 11 AA711 MET B1424 VAL B1426 1 N VAL B1425 O GLN B1444 SHEET 1 AA8 2 VAL B1255 GLU B1257 0 SHEET 2 AA8 2 LYS B1265 PHE B1267 -1 O GLN B1266 N PHE B1256 SHEET 1 AA9 5 VAL B1341 ALA B1343 0 SHEET 2 AA9 5 VAL B1304 PRO B1308 1 N ILE B1306 O ARG B1342 SHEET 3 AA9 5 ILE B1365 VAL B1369 1 O LEU B1367 N VAL B1305 SHEET 4 AA9 5 GLN B1378 ARG B1383 -1 O VAL B1380 N GLU B1368 SHEET 5 AA9 5 LYS B1389 ALA B1393 -1 O LEU B1390 N ALA B1381 LINK OE1 GLN A1237 MG MG A2605 1555 1555 2.57 LINK SG CYS A1448 ZN ZN A2603 1555 1555 2.27 LINK SG CYS A1453 ZN ZN A2603 1555 1555 2.38 LINK SG CYS A1495 ZN ZN A2603 1555 1555 2.37 LINK SG CYS A1497 ZN ZN A2603 1555 1555 2.38 LINK O1G ATP A2602 MG MG A2604 1555 1555 2.38 LINK O2B ATP A2602 MG MG A2604 1555 1555 2.45 LINK O2G ATP A2602 MG MG A2605 1555 1555 2.53 LINK O1B ATP A2602 MG MG A2605 1555 1555 2.36 LINK SG CYS B1448 ZN ZN B2603 1555 1555 2.25 LINK SG CYS B1453 ZN ZN B2603 1555 1555 2.43 LINK O3G ATP B2602 MG MG B2604 1555 1555 2.82 LINK O1B ATP B2602 MG MG B2604 1555 1555 2.67 LINK O2B ATP B2602 MG MG B2605 1555 1555 2.59 CISPEP 1 LEU A 1140 PRO A 1141 0 -1.45 CISPEP 2 LEU B 1140 PRO B 1141 0 -0.63 CRYST1 71.563 92.380 86.059 90.00 108.72 90.00 P 1 21 1 4 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 0.013974 0.000000 0.004735 0.00000 SCALE2 0.000000 0.010825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012269 0.00000