HEADER TOXIN 23-JUL-19 6PWH TITLE CYSTAL STRUCTURE OF MYOTOXIN II FROM BOTHROPS MOOJENI CO-CRYSTALLIZED TITLE 2 WITH VARESPLADIB (LY315920) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC PHOSPHOLIPASE A2 HOMOLOG 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SVPLA2 HOMOLOG,M-VI,MJTX-II,MYOTOXIN II SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOTHROPS MOOJENI; SOURCE 3 ORGANISM_COMMON: LANCE-HEADED VIPER; SOURCE 4 ORGANISM_TAXID: 98334; SOURCE 5 TISSUE: VENOM GLAND KEYWDS MYOTOXIN II, MJTX-II, LYS49-PLA2, VARESPLADIB, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR G.H.M.SALVADOR,M.R.M.FONTES REVDAT 3 11-OCT-23 6PWH 1 REMARK REVDAT 2 17-MAR-21 6PWH 1 HETSYN REVDAT 1 04-DEC-19 6PWH 0 JRNL AUTH G.H.M.SALVADOR,A.A.S.GOMES,W.BRYAN-QUIROS,J.FERNANDEZ, JRNL AUTH 2 M.R.LEWIN,J.M.GUTIERREZ,B.LOMONTE,M.R.M.FONTES JRNL TITL STRUCTURAL BASIS FOR PHOSPHOLIPASE A2-LIKE TOXIN INHIBITION JRNL TITL 2 BY THE SYNTHETIC COMPOUND VARESPLADIB (LY315920). JRNL REF SCI REP V. 9 17203 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 31748642 JRNL DOI 10.1038/S41598-019-53755-5 REMARK 2 REMARK 2 RESOLUTION. 1.75 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 25477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1254 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 33.4380 - 3.6372 0.98 2773 141 0.1874 0.1842 REMARK 3 2 3.6372 - 2.8875 0.99 2712 138 0.2051 0.2450 REMARK 3 3 2.8875 - 2.5226 1.00 2740 145 0.2259 0.3072 REMARK 3 4 2.5226 - 2.2921 1.00 2698 140 0.2306 0.2306 REMARK 3 5 2.2921 - 2.1278 0.99 2732 142 0.2392 0.2431 REMARK 3 6 2.1278 - 2.0024 0.99 2667 140 0.2491 0.2604 REMARK 3 7 2.0024 - 1.9021 0.99 2665 139 0.2686 0.2987 REMARK 3 8 1.9021 - 1.8193 0.98 2671 135 0.2645 0.3006 REMARK 3 9 1.8193 - 1.7493 0.95 2565 134 0.2906 0.2917 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.04 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 : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.9467 -3.2614 75.7691 REMARK 3 T TENSOR REMARK 3 T11: 0.2718 T22: 0.2184 REMARK 3 T33: 0.2040 T12: 0.0339 REMARK 3 T13: 0.0033 T23: -0.0550 REMARK 3 L TENSOR REMARK 3 L11: 8.0089 L22: 4.7295 REMARK 3 L33: 4.0006 L12: 1.4240 REMARK 3 L13: -0.6943 L23: -1.5871 REMARK 3 S TENSOR REMARK 3 S11: -0.0488 S12: 0.3223 S13: -0.0949 REMARK 3 S21: 0.0728 S22: 0.0154 S23: -0.5770 REMARK 3 S31: -0.1686 S32: -0.0388 S33: -0.0327 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 75 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3594 1.9667 67.3050 REMARK 3 T TENSOR REMARK 3 T11: 0.5016 T22: 0.7548 REMARK 3 T33: 0.8923 T12: -0.0453 REMARK 3 T13: 0.2302 T23: 0.1049 REMARK 3 L TENSOR REMARK 3 L11: 4.7051 L22: 4.7316 REMARK 3 L33: 7.3702 L12: -0.6309 REMARK 3 L13: 4.3038 L23: -4.4829 REMARK 3 S TENSOR REMARK 3 S11: 0.0564 S12: 1.6192 S13: 0.6690 REMARK 3 S21: -0.2131 S22: -0.0703 S23: -0.5551 REMARK 3 S31: -0.2534 S32: 0.9197 S33: 0.0077 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 89 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.5655 -6.8882 79.5783 REMARK 3 T TENSOR REMARK 3 T11: 0.3075 T22: 0.2191 REMARK 3 T33: 0.3402 T12: 0.0068 REMARK 3 T13: 0.0050 T23: -0.0452 REMARK 3 L TENSOR REMARK 3 L11: 8.0204 L22: 2.8729 REMARK 3 L33: 3.6089 L12: 0.9009 REMARK 3 L13: 0.0609 L23: -2.4183 REMARK 3 S TENSOR REMARK 3 S11: 0.2216 S12: -0.3599 S13: -0.6346 REMARK 3 S21: 0.1925 S22: -0.2586 S23: -0.6509 REMARK 3 S31: -0.0613 S32: 0.1602 S33: 0.0446 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.2490 -5.5881 77.6300 REMARK 3 T TENSOR REMARK 3 T11: 0.2881 T22: 0.5967 REMARK 3 T33: 0.3754 T12: -0.0095 REMARK 3 T13: -0.0296 T23: 0.1026 REMARK 3 L TENSOR REMARK 3 L11: 8.5066 L22: 4.3559 REMARK 3 L33: 4.1754 L12: 0.4459 REMARK 3 L13: -0.2858 L23: 0.1371 REMARK 3 S TENSOR REMARK 3 S11: 0.0526 S12: 0.6967 S13: 0.0782 REMARK 3 S21: -0.0868 S22: -0.0956 S23: 0.3991 REMARK 3 S31: -0.1800 S32: -0.3619 S33: 0.0337 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 58 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.8200 -0.9915 89.9358 REMARK 3 T TENSOR REMARK 3 T11: 0.7144 T22: 1.5280 REMARK 3 T33: 0.4739 T12: -0.1780 REMARK 3 T13: 0.0909 T23: -0.4323 REMARK 3 L TENSOR REMARK 3 L11: 6.5668 L22: 3.5310 REMARK 3 L33: 1.4006 L12: 1.8524 REMARK 3 L13: 2.9941 L23: 1.1882 REMARK 3 S TENSOR REMARK 3 S11: 0.8089 S12: -3.5761 S13: 0.1220 REMARK 3 S21: 1.2669 S22: 0.0063 S23: -0.0058 REMARK 3 S31: -0.2479 S32: -0.0020 S33: -0.0425 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 89 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.8594 -4.8109 74.4746 REMARK 3 T TENSOR REMARK 3 T11: 0.3385 T22: 0.7517 REMARK 3 T33: 0.4434 T12: -0.0107 REMARK 3 T13: -0.0234 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 9.2973 L22: 1.2735 REMARK 3 L33: 4.0604 L12: 0.3820 REMARK 3 L13: -0.9468 L23: -1.5884 REMARK 3 S TENSOR REMARK 3 S11: 0.2722 S12: 1.3005 S13: 0.4191 REMARK 3 S21: -0.2785 S22: 0.0138 S23: 0.4653 REMARK 3 S31: -0.1029 S32: -0.5906 S33: -0.3006 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 6PWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000243193. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-17 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 : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.425 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 1.8.4 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25514 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.749 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.42200 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: PHASER 2.7.16 REMARK 200 STARTING MODEL: 4KF3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% V/W PEG4000, 0.1M TRIS HCL, 0.2M REMARK 280 LITHIUM SULFATE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 18.59450 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: 1910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 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 7 CD CE NZ REMARK 470 LYS A 16 CE NZ REMARK 470 LYS A 53 CE NZ REMARK 470 LYS A 69 CD CE NZ REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 LYS A 80 NZ REMARK 470 LYS A 116 CG CD CE NZ REMARK 470 LYS A 128 CE NZ REMARK 470 LYS B 7 CD CE NZ REMARK 470 LYS B 36 CD CE NZ REMARK 470 LYS B 53 CE NZ REMARK 470 LYS B 69 CG CD CE NZ REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 LYS B 78 CG CD CE NZ REMARK 470 LYS B 128 CG CD CE NZ REMARK 470 LYS B 129 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 THR A 112 O HOH A 301 2.04 REMARK 500 O HOH B 314 O HOH B 332 2.04 REMARK 500 O23 VRD A 201 O HOH A 302 2.07 REMARK 500 O HOH A 340 O HOH A 345 2.16 REMARK 500 NE ARG A 34 O HOH A 303 2.19 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 ASP A 79 -100.53 56.33 REMARK 500 GLU A 86 115.04 -20.14 REMARK 500 TYR A 119 77.49 -115.94 REMARK 500 ASP B 79 -120.61 59.52 REMARK 500 ASN B 87 66.89 -177.99 REMARK 500 ASN B 88 145.98 70.08 REMARK 500 TYR B 119 75.96 -114.13 REMARK 500 PRO B 132 42.24 -69.26 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 B 335 DISTANCE = 6.88 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue VRD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue VRD B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6B84 RELATED DB: PDB REMARK 900 NATIVE PROTEIN REMARK 900 RELATED ID: 6B80 RELATED DB: PDB REMARK 900 ACTIVE PROTEIN REMARK 900 RELATED ID: 4YV5 RELATED DB: PDB REMARK 900 PROTEIN COMPLEXED TO SURAMIN DBREF 6PWH A 1 133 UNP Q9I834 PA2H2_BOTMO 1 122 DBREF 6PWH B 1 133 UNP Q9I834 PA2H2_BOTMO 1 122 SEQRES 1 A 122 SER LEU PHE GLU LEU GLY LYS MET ILE LEU GLN GLU THR SEQRES 2 A 122 GLY LYS ASN PRO ALA LYS SER TYR GLY VAL TYR GLY CYS SEQRES 3 A 122 ASN CYS GLY VAL GLY GLY ARG GLY LYS PRO LYS ASP ALA SEQRES 4 A 122 THR ASP ARG CYS CYS TYR VAL HIS LYS CYS CYS TYR LYS SEQRES 5 A 122 LYS LEU THR GLY CYS ASP PRO LYS LYS ASP ARG TYR SER SEQRES 6 A 122 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY GLU ASN SEQRES 7 A 122 ASN SER CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 A 122 VAL ALA ILE CYS LEU ARG GLU ASN LEU ASP THR TYR ASN SEQRES 9 A 122 LYS LYS TYR ARG TYR ASN TYR LEU LYS PRO PHE CYS LYS SEQRES 10 A 122 LYS ALA ASP PRO CYS SEQRES 1 B 122 SER LEU PHE GLU LEU GLY LYS MET ILE LEU GLN GLU THR SEQRES 2 B 122 GLY LYS ASN PRO ALA LYS SER TYR GLY VAL TYR GLY CYS SEQRES 3 B 122 ASN CYS GLY VAL GLY GLY ARG GLY LYS PRO LYS ASP ALA SEQRES 4 B 122 THR ASP ARG CYS CYS TYR VAL HIS LYS CYS CYS TYR LYS SEQRES 5 B 122 LYS LEU THR GLY CYS ASP PRO LYS LYS ASP ARG TYR SER SEQRES 6 B 122 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY GLU ASN SEQRES 7 B 122 ASN SER CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 B 122 VAL ALA ILE CYS LEU ARG GLU ASN LEU ASP THR TYR ASN SEQRES 9 B 122 LYS LYS TYR ARG TYR ASN TYR LEU LYS PRO PHE CYS LYS SEQRES 10 B 122 LYS ALA ASP PRO CYS HET VRD A 201 28 HET DMS A 202 4 HET DMS A 203 4 HET VRD B 201 28 HETNAM VRD ({3-[AMINO(OXO)ACETYL]-1-BENZYL-2-ETHYL-1H-INDOL-4- HETNAM 2 VRD YL}OXY)ACETIC ACID HETNAM DMS DIMETHYL SULFOXIDE HETSYN VRD VARESPLADIB FORMUL 3 VRD 2(C21 H20 N2 O5) FORMUL 4 DMS 2(C2 H6 O S) FORMUL 7 HOH *93(H2 O) HELIX 1 AA1 SER A 1 GLY A 15 1 14 HELIX 2 AA2 ASN A 17 GLY A 23 1 7 HELIX 3 AA3 ASP A 39 LYS A 57 1 16 HELIX 4 AA4 ASN A 88 ASN A 109 1 21 HELIX 5 AA5 LEU A 110 TYR A 113 5 4 HELIX 6 AA6 ASN A 114 ARG A 118 5 5 HELIX 7 AA7 LEU A 122 CYS A 127 5 5 HELIX 8 AA8 LEU B 2 GLY B 15 1 13 HELIX 9 AA9 ASN B 17 GLY B 23 1 7 HELIX 10 AB1 ASP B 39 LYS B 57 1 16 HELIX 11 AB2 ASN B 87 ASN B 109 1 22 HELIX 12 AB3 LEU B 110 TYR B 113 5 4 HELIX 13 AB4 ASN B 114 ARG B 118 5 5 HELIX 14 AB5 LEU B 122 CYS B 127 5 5 SHEET 1 AA1 2 TYR A 75 LYS A 78 0 SHEET 2 AA1 2 THR A 81 CYS A 84 -1 O THR A 81 N LYS A 78 SHEET 1 AA2 2 TYR B 75 LYS B 78 0 SHEET 2 AA2 2 THR B 81 CYS B 84 -1 O VAL B 83 N SER B 76 SSBOND 1 CYS A 27 CYS A 127 1555 1555 2.03 SSBOND 2 CYS A 29 CYS A 45 1555 1555 2.03 SSBOND 3 CYS A 44 CYS A 105 1555 1555 2.04 SSBOND 4 CYS A 50 CYS A 133 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.03 SSBOND 6 CYS A 61 CYS A 90 1555 1555 2.03 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.03 SSBOND 8 CYS B 27 CYS B 127 1555 1555 2.03 SSBOND 9 CYS B 29 CYS B 45 1555 1555 2.04 SSBOND 10 CYS B 44 CYS B 105 1555 1555 2.03 SSBOND 11 CYS B 50 CYS B 133 1555 1555 2.03 SSBOND 12 CYS B 51 CYS B 98 1555 1555 2.04 SSBOND 13 CYS B 61 CYS B 90 1555 1555 2.03 SSBOND 14 CYS B 84 CYS B 96 1555 1555 2.03 SITE 1 AC1 13 LEU A 2 GLY A 6 ALA A 19 TYR A 22 SITE 2 AC1 13 ASN A 28 CYS A 29 GLY A 30 CYS A 45 SITE 3 AC1 13 HIS A 48 LYS A 49 TYR A 52 HOH A 302 SITE 4 AC1 13 PHE B 126 SITE 1 AC2 3 LYS A 116 ASN A 120 HOH A 327 SITE 1 AC3 7 LYS A 57 THR A 59 GLY A 60 CYS A 90 SITE 2 AC3 7 GLU A 94 LEU A 110 ASP A 111 SITE 1 AC4 12 PHE A 126 LEU B 2 GLY B 6 ALA B 19 SITE 2 AC4 12 TYR B 22 ASN B 28 CYS B 29 GLY B 30 SITE 3 AC4 12 CYS B 45 HIS B 48 LYS B 49 TYR B 52 CRYST1 54.864 37.189 68.681 90.00 114.39 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 0.018227 0.000000 0.008264 0.00000 SCALE2 0.000000 0.026890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015987 0.00000