HEADER LIGASE 24-JUN-19 6KBF TITLE CRYSTAL STRUCTURE OF PLASMODIUM LYSYL-TRNA SYNTHETASE IN COMPLEX WITH TITLE 2 A CLADOSPORIN DERIVATIVE 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE--TRNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LYSYL-TRNA SYNTHETASE; COMPND 5 EC: 6.1.1.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM (ISOLATE NF54); SOURCE 3 ORGANISM_TAXID: 5843; SOURCE 4 STRAIN: ISOLATE NF54; SOURCE 5 GENE: PFNF54_04763; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COMPLEX, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHOU,P.FANG REVDAT 3 22-NOV-23 6KBF 1 REMARK REVDAT 2 06-MAY-20 6KBF 1 JRNL REVDAT 1 08-APR-20 6KBF 0 JRNL AUTH J.ZHOU,L.ZHENG,Z.HEI,W.LI,J.WANG,B.YU,P.FANG JRNL TITL ATOMIC RESOLUTION ANALYSES OF ISOCOUMARIN DERIVATIVES FOR JRNL TITL 2 INHIBITION OF LYSYL-TRNA SYNTHETASE. JRNL REF ACS CHEM.BIOL. V. 15 1016 2020 JRNL REFN ESSN 1554-8937 JRNL PMID 32195573 JRNL DOI 10.1021/ACSCHEMBIO.0C00032 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 87607 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 4255 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 43.8569 - 4.1355 0.99 8557 416 0.1563 0.1839 REMARK 3 2 4.1355 - 3.2828 1.00 8405 454 0.1579 0.1866 REMARK 3 3 3.2828 - 2.8680 1.00 8420 436 0.1765 0.2100 REMARK 3 4 2.8680 - 2.6058 1.00 8371 422 0.1819 0.2250 REMARK 3 5 2.6058 - 2.4190 1.00 8391 426 0.1898 0.2419 REMARK 3 6 2.4190 - 2.2764 1.00 8401 403 0.1991 0.2486 REMARK 3 7 2.2764 - 2.1624 1.00 8362 437 0.2090 0.2569 REMARK 3 8 2.1624 - 2.0683 1.00 8359 431 0.2296 0.2741 REMARK 3 9 2.0683 - 1.9886 1.00 8408 409 0.2506 0.3125 REMARK 3 10 1.9886 - 1.9200 0.92 7678 421 0.2782 0.3018 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.95 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -50.9080 -8.8197 23.3897 REMARK 3 T TENSOR REMARK 3 T11: 0.2685 T22: 0.2186 REMARK 3 T33: 0.2575 T12: -0.0264 REMARK 3 T13: 0.0947 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.5753 L22: 1.1801 REMARK 3 L33: 1.1873 L12: -0.1843 REMARK 3 L13: 0.2809 L23: -0.1825 REMARK 3 S TENSOR REMARK 3 S11: 0.0249 S12: 0.0231 S13: 0.0466 REMARK 3 S21: -0.3934 S22: -0.0430 S23: -0.2879 REMARK 3 S31: 0.0811 S32: 0.1798 S33: -0.0154 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 6KBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012665. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 47.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 1.31300 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: MOLREP REMARK 200 STARTING MODEL: 4YCV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRI-SODIUM CITRATE, PEG 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 35.41100 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: 10600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 76 REMARK 465 GLU A 77 REMARK 465 VAL A 78 REMARK 465 ASN A 583 REMARK 465 GLY A 584 REMARK 465 GLY A 585 REMARK 465 HIS A 586 REMARK 465 HIS A 587 REMARK 465 HIS A 588 REMARK 465 HIS A 589 REMARK 465 HIS A 590 REMARK 465 HIS A 591 REMARK 465 MET B 76 REMARK 465 GLU B 77 REMARK 465 VAL B 78 REMARK 465 ALA B 582 REMARK 465 ASN B 583 REMARK 465 GLY B 584 REMARK 465 GLY B 585 REMARK 465 HIS B 586 REMARK 465 HIS B 587 REMARK 465 HIS B 588 REMARK 465 HIS B 589 REMARK 465 HIS B 590 REMARK 465 HIS B 591 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 ARG A 81 CD NE CZ NH1 NH2 REMARK 470 LYS A 89 CD CE NZ REMARK 470 LYS A 97 CG CD CE NZ REMARK 470 ILE A 99 CG1 CG2 CD1 REMARK 470 GLN A 147 CG CD OE1 NE2 REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 GLU A 173 CG CD OE1 OE2 REMARK 470 GLU A 179 CD OE1 OE2 REMARK 470 LYS A 183 CD CE NZ REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 MET A 220 SD CE REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 TYR A 225 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 ASP A 229 CG OD1 OD2 REMARK 470 GLU A 245 CG CD OE1 OE2 REMARK 470 GLU A 386 CG CD OE1 OE2 REMARK 470 GLN A 388 CG CD OE1 NE2 REMARK 470 LYS A 433 CG CD CE NZ REMARK 470 GLU A 434 CD OE1 OE2 REMARK 470 LYS A 436 CG CD CE NZ REMARK 470 LYS A 519 CG CD CE NZ REMARK 470 ARG A 525 CZ NH1 NH2 REMARK 470 LYS A 527 CD CE NZ REMARK 470 GLN A 534 CG CD OE1 NE2 REMARK 470 ARG B 81 CD NE CZ NH1 NH2 REMARK 470 LYS B 89 CD CE NZ REMARK 470 LYS B 97 CG CD CE NZ REMARK 470 ILE B 99 CG1 CG2 CD1 REMARK 470 GLN B 147 CD OE1 NE2 REMARK 470 LYS B 200 CG CD CE NZ REMARK 470 LYS B 201 CG CD CE NZ REMARK 470 MET B 223 CG SD CE REMARK 470 LYS B 224 CG CD CE NZ REMARK 470 TYR B 225 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 228 CG CD CE NZ REMARK 470 ASP B 229 CG OD1 OD2 REMARK 470 GLU B 245 CG CD OE1 OE2 REMARK 470 ASN B 286 CG OD1 ND2 REMARK 470 GLU B 386 CG CD OE1 OE2 REMARK 470 VAL B 404 CG1 CG2 REMARK 470 ILE B 407 CG1 CG2 CD1 REMARK 470 LYS B 409 CG CD CE NZ REMARK 470 VAL B 410 CG1 CG2 REMARK 470 ASN B 412 CG OD1 ND2 REMARK 470 THR B 413 OG1 CG2 REMARK 470 ILE B 414 CG1 CG2 CD1 REMARK 470 LEU B 415 CG CD1 CD2 REMARK 470 GLU B 416 CG CD OE1 OE2 REMARK 470 GLN B 417 CG CD OE1 NE2 REMARK 470 PRO B 418 CG CD REMARK 470 GLU B 423 CG CD OE1 OE2 REMARK 470 THR B 424 OG1 CG2 REMARK 470 ILE B 425 CG1 CG2 CD1 REMARK 470 GLU B 426 CG CD OE1 OE2 REMARK 470 LYS B 427 CG CD CE NZ REMARK 470 MET B 428 CG SD CE REMARK 470 ILE B 429 CG1 CG2 CD1 REMARK 470 ASN B 430 CG OD1 ND2 REMARK 470 ILE B 431 CG1 CG2 CD1 REMARK 470 ILE B 432 CG1 CG2 CD1 REMARK 470 LYS B 433 CG CD CE NZ REMARK 470 GLU B 434 CD OE1 OE2 REMARK 470 LYS B 436 CG CD CE NZ REMARK 470 ILE B 437 CG1 CG2 CD1 REMARK 470 GLU B 438 CG CD OE1 OE2 REMARK 470 LEU B 439 CG CD1 CD2 REMARK 470 LYS B 447 CG CD CE NZ REMARK 470 LEU B 448 CG CD1 CD2 REMARK 470 LEU B 452 CG CD1 CD2 REMARK 470 PHE B 456 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE B 512 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 515 CG CD CE NZ REMARK 470 PHE B 518 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 519 CG CD CE NZ REMARK 470 LEU B 520 CG CD1 CD2 REMARK 470 GLN B 521 CG CD OE1 NE2 REMARK 470 GLN B 522 CG CD OE1 NE2 REMARK 470 LYS B 523 CG CD CE NZ REMARK 470 ASP B 524 CG OD1 OD2 REMARK 470 ARG B 525 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 526 CG CD OE1 OE2 REMARK 470 LYS B 527 CG CD CE NZ REMARK 470 ASP B 529 CG OD1 OD2 REMARK 470 GLU B 531 CG CD OE1 OE2 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 GLN A 147 -9.57 65.75 REMARK 500 SER A 215 116.96 -161.47 REMARK 500 ASN A 331 77.13 -100.46 REMARK 500 LEU B 128 74.37 -105.20 REMARK 500 SER B 215 116.28 -160.17 REMARK 500 GLU B 332 -158.81 -148.29 REMARK 500 ILE B 457 -50.39 -128.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1117 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A1118 DISTANCE = 6.67 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LYS A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D4X A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LYS B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D4X B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 605 DBREF 6KBF A 77 583 UNP W7JP72 W7JP72_PLAFO 15 521 DBREF 6KBF B 77 583 UNP W7JP72 W7JP72_PLAFO 15 521 SEQADV 6KBF MET A 76 UNP W7JP72 INITIATING METHIONINE SEQADV 6KBF GLY A 584 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF GLY A 585 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS A 586 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS A 587 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS A 588 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS A 589 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS A 590 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS A 591 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF MET B 76 UNP W7JP72 INITIATING METHIONINE SEQADV 6KBF GLY B 584 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF GLY B 585 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS B 586 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS B 587 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS B 588 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS B 589 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS B 590 UNP W7JP72 EXPRESSION TAG SEQADV 6KBF HIS B 591 UNP W7JP72 EXPRESSION TAG SEQRES 1 A 516 MET GLU VAL ASP PRO ARG LEU TYR PHE GLU ASN ARG SER SEQRES 2 A 516 LYS PHE ILE GLN ASP GLN LYS ASP LYS GLY ILE ASN PRO SEQRES 3 A 516 TYR PRO HIS LYS PHE GLU ARG THR ILE SER ILE PRO GLU SEQRES 4 A 516 PHE ILE GLU LYS TYR LYS ASP LEU GLY ASN GLY GLU HIS SEQRES 5 A 516 LEU GLU ASP THR ILE LEU ASN ILE THR GLY ARG ILE MET SEQRES 6 A 516 ARG VAL SER ALA SER GLY GLN LYS LEU ARG PHE PHE ASP SEQRES 7 A 516 LEU VAL GLY ASP GLY GLU LYS ILE GLN VAL LEU ALA ASN SEQRES 8 A 516 TYR SER PHE HIS ASN HIS GLU LYS GLY ASN PHE ALA GLU SEQRES 9 A 516 CYS TYR ASP LYS ILE ARG ARG GLY ASP ILE VAL GLY ILE SEQRES 10 A 516 VAL GLY PHE PRO GLY LYS SER LYS LYS GLY GLU LEU SER SEQRES 11 A 516 ILE PHE PRO LYS GLU THR ILE LEU LEU SER ALA CYS LEU SEQRES 12 A 516 HIS MET LEU PRO MET LYS TYR GLY LEU LYS ASP THR GLU SEQRES 13 A 516 ILE ARG TYR ARG GLN ARG TYR LEU ASP LEU LEU ILE ASN SEQRES 14 A 516 GLU SER SER ARG HIS THR PHE VAL THR ARG THR LYS ILE SEQRES 15 A 516 ILE ASN PHE LEU ARG ASN PHE LEU ASN GLU ARG GLY PHE SEQRES 16 A 516 PHE GLU VAL GLU THR PRO MET MET ASN LEU ILE ALA GLY SEQRES 17 A 516 GLY ALA ASN ALA ARG PRO PHE ILE THR HIS HIS ASN ASP SEQRES 18 A 516 LEU ASP LEU ASP LEU TYR LEU ARG ILE ALA THR GLU LEU SEQRES 19 A 516 PRO LEU LYS MET LEU ILE VAL GLY GLY ILE ASP LYS VAL SEQRES 20 A 516 TYR GLU ILE GLY LYS VAL PHE ARG ASN GLU GLY ILE ASP SEQRES 21 A 516 ASN THR HIS ASN PRO GLU PHE THR SER CYS GLU PHE TYR SEQRES 22 A 516 TRP ALA TYR ALA ASP TYR ASN ASP LEU ILE LYS TRP SER SEQRES 23 A 516 GLU ASP PHE PHE SER GLN LEU VAL TYR HIS LEU PHE GLY SEQRES 24 A 516 THR TYR LYS ILE SER TYR ASN LYS ASP GLY PRO GLU ASN SEQRES 25 A 516 GLN PRO ILE GLU ILE ASP PHE THR PRO PRO TYR PRO LYS SEQRES 26 A 516 VAL SER ILE VAL GLU GLU ILE GLU LYS VAL THR ASN THR SEQRES 27 A 516 ILE LEU GLU GLN PRO PHE ASP SER ASN GLU THR ILE GLU SEQRES 28 A 516 LYS MET ILE ASN ILE ILE LYS GLU HIS LYS ILE GLU LEU SEQRES 29 A 516 PRO ASN PRO PRO THR ALA ALA LYS LEU LEU ASP GLN LEU SEQRES 30 A 516 ALA SER HIS PHE ILE GLU ASN LYS TYR ASN ASP LYS PRO SEQRES 31 A 516 PHE PHE ILE VAL GLU HIS PRO GLN ILE MET SER PRO LEU SEQRES 32 A 516 ALA LYS TYR HIS ARG THR LYS PRO GLY LEU THR GLU ARG SEQRES 33 A 516 LEU GLU MET PHE ILE CYS GLY LYS GLU VAL LEU ASN ALA SEQRES 34 A 516 TYR THR GLU LEU ASN ASP PRO PHE LYS GLN LYS GLU CYS SEQRES 35 A 516 PHE LYS LEU GLN GLN LYS ASP ARG GLU LYS GLY ASP THR SEQRES 36 A 516 GLU ALA ALA GLN LEU ASP SER ALA PHE CYS THR SER LEU SEQRES 37 A 516 GLU TYR GLY LEU PRO PRO THR GLY GLY LEU GLY LEU GLY SEQRES 38 A 516 ILE ASP ARG ILE THR MET PHE LEU THR ASN LYS ASN SER SEQRES 39 A 516 ILE LYS ASP VAL ILE LEU PHE PRO THR MET ARG PRO ALA SEQRES 40 A 516 ASN GLY GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 516 MET GLU VAL ASP PRO ARG LEU TYR PHE GLU ASN ARG SER SEQRES 2 B 516 LYS PHE ILE GLN ASP GLN LYS ASP LYS GLY ILE ASN PRO SEQRES 3 B 516 TYR PRO HIS LYS PHE GLU ARG THR ILE SER ILE PRO GLU SEQRES 4 B 516 PHE ILE GLU LYS TYR LYS ASP LEU GLY ASN GLY GLU HIS SEQRES 5 B 516 LEU GLU ASP THR ILE LEU ASN ILE THR GLY ARG ILE MET SEQRES 6 B 516 ARG VAL SER ALA SER GLY GLN LYS LEU ARG PHE PHE ASP SEQRES 7 B 516 LEU VAL GLY ASP GLY GLU LYS ILE GLN VAL LEU ALA ASN SEQRES 8 B 516 TYR SER PHE HIS ASN HIS GLU LYS GLY ASN PHE ALA GLU SEQRES 9 B 516 CYS TYR ASP LYS ILE ARG ARG GLY ASP ILE VAL GLY ILE SEQRES 10 B 516 VAL GLY PHE PRO GLY LYS SER LYS LYS GLY GLU LEU SER SEQRES 11 B 516 ILE PHE PRO LYS GLU THR ILE LEU LEU SER ALA CYS LEU SEQRES 12 B 516 HIS MET LEU PRO MET LYS TYR GLY LEU LYS ASP THR GLU SEQRES 13 B 516 ILE ARG TYR ARG GLN ARG TYR LEU ASP LEU LEU ILE ASN SEQRES 14 B 516 GLU SER SER ARG HIS THR PHE VAL THR ARG THR LYS ILE SEQRES 15 B 516 ILE ASN PHE LEU ARG ASN PHE LEU ASN GLU ARG GLY PHE SEQRES 16 B 516 PHE GLU VAL GLU THR PRO MET MET ASN LEU ILE ALA GLY SEQRES 17 B 516 GLY ALA ASN ALA ARG PRO PHE ILE THR HIS HIS ASN ASP SEQRES 18 B 516 LEU ASP LEU ASP LEU TYR LEU ARG ILE ALA THR GLU LEU SEQRES 19 B 516 PRO LEU LYS MET LEU ILE VAL GLY GLY ILE ASP LYS VAL SEQRES 20 B 516 TYR GLU ILE GLY LYS VAL PHE ARG ASN GLU GLY ILE ASP SEQRES 21 B 516 ASN THR HIS ASN PRO GLU PHE THR SER CYS GLU PHE TYR SEQRES 22 B 516 TRP ALA TYR ALA ASP TYR ASN ASP LEU ILE LYS TRP SER SEQRES 23 B 516 GLU ASP PHE PHE SER GLN LEU VAL TYR HIS LEU PHE GLY SEQRES 24 B 516 THR TYR LYS ILE SER TYR ASN LYS ASP GLY PRO GLU ASN SEQRES 25 B 516 GLN PRO ILE GLU ILE ASP PHE THR PRO PRO TYR PRO LYS SEQRES 26 B 516 VAL SER ILE VAL GLU GLU ILE GLU LYS VAL THR ASN THR SEQRES 27 B 516 ILE LEU GLU GLN PRO PHE ASP SER ASN GLU THR ILE GLU SEQRES 28 B 516 LYS MET ILE ASN ILE ILE LYS GLU HIS LYS ILE GLU LEU SEQRES 29 B 516 PRO ASN PRO PRO THR ALA ALA LYS LEU LEU ASP GLN LEU SEQRES 30 B 516 ALA SER HIS PHE ILE GLU ASN LYS TYR ASN ASP LYS PRO SEQRES 31 B 516 PHE PHE ILE VAL GLU HIS PRO GLN ILE MET SER PRO LEU SEQRES 32 B 516 ALA LYS TYR HIS ARG THR LYS PRO GLY LEU THR GLU ARG SEQRES 33 B 516 LEU GLU MET PHE ILE CYS GLY LYS GLU VAL LEU ASN ALA SEQRES 34 B 516 TYR THR GLU LEU ASN ASP PRO PHE LYS GLN LYS GLU CYS SEQRES 35 B 516 PHE LYS LEU GLN GLN LYS ASP ARG GLU LYS GLY ASP THR SEQRES 36 B 516 GLU ALA ALA GLN LEU ASP SER ALA PHE CYS THR SER LEU SEQRES 37 B 516 GLU TYR GLY LEU PRO PRO THR GLY GLY LEU GLY LEU GLY SEQRES 38 B 516 ILE ASP ARG ILE THR MET PHE LEU THR ASN LYS ASN SER SEQRES 39 B 516 ILE LYS ASP VAL ILE LEU PHE PRO THR MET ARG PRO ALA SEQRES 40 B 516 ASN GLY GLY HIS HIS HIS HIS HIS HIS HET LYS A 601 10 HET D4X A 602 21 HET GOL A 603 6 HET GOL A 604 6 HET GOL A 605 6 HET LYS B 601 10 HET D4X B 602 21 HET GOL B 603 6 HET GOL B 604 6 HET DMS B 605 4 HETNAM LYS LYSINE HETNAM D4X (3~{S})-3-[[(1~{S},3~{S})-3-METHYLCYCLOHEXYL]METHYL]-6, HETNAM 2 D4X 8-BIS(OXIDANYL)-3,4-DIHYDRO-2~{H}-ISOQUINOLIN-1-ONE HETNAM GOL GLYCEROL HETNAM DMS DIMETHYL SULFOXIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 LYS 2(C6 H15 N2 O2 1+) FORMUL 4 D4X 2(C17 H23 N O3) FORMUL 5 GOL 5(C3 H8 O3) FORMUL 12 DMS C2 H6 O S FORMUL 13 HOH *660(H2 O) HELIX 1 AA1 ASP A 79 LYS A 97 1 19 HELIX 2 AA2 SER A 111 LYS A 120 1 10 HELIX 3 AA3 SER A 168 HIS A 170 5 3 HELIX 4 AA4 ASN A 171 GLY A 175 5 5 HELIX 5 AA5 ASN A 176 LYS A 183 1 8 HELIX 6 AA6 GLU A 231 GLN A 236 1 6 HELIX 7 AA7 GLN A 236 ASN A 244 1 9 HELIX 8 AA8 ASN A 244 ARG A 268 1 25 HELIX 9 AA9 THR A 307 GLY A 317 1 11 HELIX 10 AB1 ASP A 353 GLY A 374 1 22 HELIX 11 AB2 ILE A 403 ASN A 412 1 10 HELIX 12 AB3 SER A 421 HIS A 435 1 15 HELIX 13 AB4 THR A 444 ILE A 457 1 14 HELIX 14 AB5 PRO A 472 SER A 476 5 5 HELIX 15 AB6 ASP A 510 GLY A 528 1 19 HELIX 16 AB7 ASP A 536 GLU A 544 1 9 HELIX 17 AB8 ILE A 557 THR A 565 1 9 HELIX 18 AB9 SER A 569 VAL A 573 5 5 HELIX 19 AC1 PRO B 80 GLY B 98 1 19 HELIX 20 AC2 SER B 111 LYS B 120 1 10 HELIX 21 AC3 SER B 168 HIS B 170 5 3 HELIX 22 AC4 ASN B 171 GLY B 175 5 5 HELIX 23 AC5 ASN B 176 LYS B 183 1 8 HELIX 24 AC6 GLU B 231 GLN B 236 1 6 HELIX 25 AC7 GLN B 236 ASN B 244 1 9 HELIX 26 AC8 ASN B 244 ARG B 268 1 25 HELIX 27 AC9 THR B 307 GLY B 317 1 11 HELIX 28 AD1 ASP B 353 GLY B 374 1 22 HELIX 29 AD2 ILE B 403 ASN B 412 1 10 HELIX 30 AD3 SER B 421 HIS B 435 1 15 HELIX 31 AD4 THR B 444 ILE B 457 1 14 HELIX 32 AD5 PRO B 472 SER B 476 5 5 HELIX 33 AD6 ASP B 510 GLU B 526 1 17 HELIX 34 AD7 ASP B 536 GLU B 544 1 9 HELIX 35 AD8 ILE B 557 THR B 565 1 9 HELIX 36 AD9 SER B 569 VAL B 573 5 5 SHEET 1 AA1 6 LEU A 133 ALA A 144 0 SHEET 2 AA1 6 LEU A 149 GLY A 156 -1 O VAL A 155 N ARG A 138 SHEET 3 AA1 6 GLU A 159 ASN A 166 -1 O ILE A 161 N LEU A 154 SHEET 4 AA1 6 LEU A 204 SER A 215 1 O ILE A 206 N LEU A 164 SHEET 5 AA1 6 ILE A 189 LYS A 198 -1 N VAL A 193 O LYS A 209 SHEET 6 AA1 6 LEU A 133 ALA A 144 -1 N LEU A 133 O GLY A 194 SHEET 1 AA2 8 PHE A 271 GLU A 272 0 SHEET 2 AA2 8 LYS A 321 PHE A 329 1 O LYS A 321 N PHE A 271 SHEET 3 AA2 8 GLU A 341 ALA A 350 -1 O SER A 344 N GLY A 326 SHEET 4 AA2 8 THR A 550 GLY A 556 -1 O GLY A 551 N TRP A 349 SHEET 5 AA2 8 LYS A 499 THR A 506 -1 N ASN A 503 O GLY A 554 SHEET 6 AA2 8 ARG A 491 ILE A 496 -1 N MET A 494 O VAL A 501 SHEET 7 AA2 8 PHE A 466 VAL A 469 -1 N PHE A 466 O PHE A 495 SHEET 8 AA2 8 LYS A 400 SER A 402 1 N VAL A 401 O PHE A 467 SHEET 1 AA3 3 MET A 278 ASN A 279 0 SHEET 2 AA3 3 LEU A 299 LEU A 303 -1 O TYR A 302 N ASN A 279 SHEET 3 AA3 3 ILE A 291 HIS A 294 -1 N HIS A 294 O LEU A 299 SHEET 1 AA4 2 LYS A 377 TYR A 380 0 SHEET 2 AA4 2 ILE A 390 ASP A 393 -1 O ILE A 390 N TYR A 380 SHEET 1 AA5 6 LEU B 133 ALA B 144 0 SHEET 2 AA5 6 LEU B 149 GLY B 156 -1 O PHE B 151 N SER B 143 SHEET 3 AA5 6 GLU B 159 ASN B 166 -1 O VAL B 163 N PHE B 152 SHEET 4 AA5 6 LEU B 204 SER B 215 1 O ILE B 206 N LEU B 164 SHEET 5 AA5 6 ILE B 189 LYS B 198 -1 N VAL B 193 O LYS B 209 SHEET 6 AA5 6 LEU B 133 ALA B 144 -1 N LEU B 133 O GLY B 194 SHEET 1 AA6 8 PHE B 271 GLU B 272 0 SHEET 2 AA6 8 LYS B 321 PHE B 329 1 O TYR B 323 N PHE B 271 SHEET 3 AA6 8 GLU B 341 ALA B 350 -1 O SER B 344 N GLY B 326 SHEET 4 AA6 8 THR B 550 GLY B 556 -1 O LEU B 555 N CYS B 345 SHEET 5 AA6 8 LYS B 499 THR B 506 -1 N ASN B 503 O GLY B 554 SHEET 6 AA6 8 ARG B 491 ILE B 496 -1 N LEU B 492 O ALA B 504 SHEET 7 AA6 8 PHE B 466 VAL B 469 -1 N ILE B 468 O GLU B 493 SHEET 8 AA6 8 LYS B 400 SER B 402 1 N VAL B 401 O PHE B 467 SHEET 1 AA7 3 MET B 278 ASN B 279 0 SHEET 2 AA7 3 LEU B 299 LEU B 303 -1 O TYR B 302 N ASN B 279 SHEET 3 AA7 3 ILE B 291 HIS B 294 -1 N THR B 292 O LEU B 301 SHEET 1 AA8 2 LYS B 377 TYR B 380 0 SHEET 2 AA8 2 ILE B 390 ASP B 393 -1 O ILE B 392 N ILE B 378 CISPEP 1 PRO A 396 PRO A 397 0 0.19 CISPEP 2 GLN A 417 PRO A 418 0 -2.63 CISPEP 3 ASN A 441 PRO A 442 0 -4.26 CISPEP 4 PRO B 396 PRO B 397 0 -1.56 CISPEP 5 ASN B 441 PRO B 442 0 -3.09 SITE 1 AC1 13 GLY A 284 ALA A 285 ALA A 306 GLU A 308 SITE 2 AC1 13 ARG A 330 GLU A 346 TYR A 348 ASN A 503 SITE 3 AC1 13 TYR A 505 GLU A 507 GLY A 552 D4X A 602 SITE 4 AC1 13 HOH A 725 SITE 1 AC2 13 ARG A 330 GLU A 332 THR A 337 HIS A 338 SITE 2 AC2 13 ASN A 339 PHE A 342 GLU A 500 LEU A 502 SITE 3 AC2 13 GLY A 554 ARG A 559 ILE A 570 LYS A 601 SITE 4 AC2 13 HOH A 888 SITE 1 AC3 10 LYS A 321 TRP A 349 ALA A 350 TYR A 351 SITE 2 AC3 10 HOH A 739 HOH A 865 LYS B 105 GLU B 107 SITE 3 AC3 10 HOH B 720 HOH B 803 SITE 1 AC4 8 ILE A 258 ARG A 262 ILE A 325 HOH A 962 SITE 2 AC4 8 ARG B 262 GLU B 272 GLU B 274 GOL B 604 SITE 1 AC5 5 TYR A 354 ASN A 355 HIS A 482 ARG A 483 SITE 2 AC5 5 GLU A 490 SITE 1 AC6 12 GLY B 284 ALA B 285 GLU B 308 ARG B 330 SITE 2 AC6 12 GLU B 346 TYR B 348 ASN B 503 TYR B 505 SITE 3 AC6 12 GLU B 507 GLY B 552 GLY B 554 HOH B 719 SITE 1 AC7 12 ARG B 330 GLU B 332 HIS B 338 ASN B 339 SITE 2 AC7 12 PHE B 342 VAL B 501 LEU B 502 GLY B 554 SITE 3 AC7 12 ARG B 559 ILE B 570 HOH B 755 HOH B 802 SITE 1 AC8 11 LYS A 105 GLU A 107 HOH A 721 HOH A 833 SITE 2 AC8 11 LYS B 321 TRP B 349 ALA B 350 TYR B 351 SITE 3 AC8 11 HOH B 724 HOH B 813 HOH B 857 SITE 1 AC9 7 ARG A 262 GLU A 272 GLU A 274 GOL A 604 SITE 2 AC9 7 ILE B 258 ARG B 262 ILE B 325 SITE 1 AD1 2 PHE A 271 ARG B 248 CRYST1 87.932 70.822 101.125 90.00 111.45 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 0.011372 0.000000 0.004468 0.00000 SCALE2 0.000000 0.014120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010625 0.00000