HEADER TRANSFERASE 02-AUG-22 8DXM
TITLE HIV-1 REVERSE TRANSCRIPTASE/RILPIVIRINE WITH BOUND FRAGMENT 4-
TITLE 2 BROMOPHENOL AT THE KNUCKLES SITE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: REVERSE TRANSCRIPTASE/RIBONUCLEASE H;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: EXORIBONUCLEASE H, P66 RT;
COMPND 5 EC: 2.7.7.49,2.7.7.7,3.1.26.13,3.1.13.2;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: P51 RT;
COMPND 10 CHAIN: B;
COMPND 11 ENGINEERED: YES;
COMPND 12 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M
SOURCE 3 SUBTYPE B (ISOLATE BH10);
SOURCE 4 ORGANISM_COMMON: HIV-1;
SOURCE 5 ORGANISM_TAXID: 11678;
SOURCE 6 STRAIN: ISOLATE BH10;
SOURCE 7 GENE: GAG-POL;
SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 10 MOL_ID: 2;
SOURCE 11 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M
SOURCE 12 SUBTYPE B (ISOLATE BH10);
SOURCE 13 ORGANISM_COMMON: HIV-1;
SOURCE 14 ORGANISM_TAXID: 11678;
SOURCE 15 STRAIN: ISOLATE BH10;
SOURCE 16 GENE: GAG-POL;
SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS HIV-1 REVERSE TRANSCRIPTASE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.CHOPRA,F.X.RUIZ,J.D.BAUMAN,E.ARNOLD
REVDAT 2 25-OCT-23 8DXM 1 REMARK
REVDAT 1 31-MAY-23 8DXM 0
JRNL AUTH A.CHOPRA,J.D.BAUMAN,F.X.RUIZ,E.ARNOLD
JRNL TITL HALO LIBRARY, A TOOL FOR RAPID IDENTIFICATION OF LIGAND
JRNL TITL 2 BINDING SITES ON PROTEINS USING CRYSTALLOGRAPHIC FRAGMENT
JRNL TITL 3 SCREENING.
JRNL REF J.MED.CHEM. V. 66 6013 2023
JRNL REFN ISSN 0022-2623
JRNL PMID 37115705
JRNL DOI 10.1021/ACS.JMEDCHEM.2C01681
REMARK 2
REMARK 2 RESOLUTION. 1.99 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX DEV_3051
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.15
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0
REMARK 3 NUMBER OF REFLECTIONS : 85451
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.197
REMARK 3 R VALUE (WORKING SET) : 0.197
REMARK 3 FREE R VALUE : 0.208
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.340
REMARK 3 FREE R VALUE TEST SET COUNT : 3848
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 42.1500 - 5.9700 0.98 6020 148 0.1718 0.1600
REMARK 3 2 5.9700 - 4.7400 0.99 6063 144 0.1795 0.1553
REMARK 3 3 4.7400 - 4.1400 0.98 5984 142 0.1593 0.1626
REMARK 3 4 4.1400 - 3.7600 0.99 6024 145 0.1664 0.1727
REMARK 3 5 3.7600 - 3.4900 0.99 6083 148 0.1791 0.1955
REMARK 3 6 3.4900 - 3.2900 0.99 6017 144 0.1919 0.2093
REMARK 3 7 3.2900 - 3.1200 0.99 6054 143 0.2072 0.2116
REMARK 3 8 3.1200 - 2.9900 0.97 5929 148 0.2154 0.2523
REMARK 3 9 2.9900 - 2.8700 0.97 5917 140 0.2160 0.2398
REMARK 3 10 2.8700 - 2.7700 0.98 6088 144 0.2112 0.2452
REMARK 3 11 2.7700 - 2.6900 0.98 5977 141 0.2261 0.2565
REMARK 3 12 2.6900 - 2.6100 0.99 6067 147 0.2284 0.2666
REMARK 3 13 2.6100 - 2.5400 0.98 5957 144 0.2179 0.2541
REMARK 3 14 2.5400 - 2.4800 0.98 6015 144 0.2231 0.2536
REMARK 3 15 2.4800 - 2.4200 0.99 6050 143 0.2263 0.2655
REMARK 3 16 2.4200 - 2.3700 0.97 5986 143 0.2224 0.2771
REMARK 3 17 2.3700 - 2.3200 0.96 5832 140 0.2214 0.2399
REMARK 3 18 2.3200 - 2.2800 0.97 5858 144 0.2276 0.2182
REMARK 3 19 2.2800 - 2.2400 0.97 6004 145 0.2326 0.2728
REMARK 3 20 2.2400 - 2.2000 0.98 5991 142 0.2314 0.2408
REMARK 3 21 2.2000 - 2.1700 0.98 6006 144 0.2374 0.2542
REMARK 3 22 2.1700 - 2.1300 0.98 6043 147 0.2445 0.2465
REMARK 3 23 2.1300 - 2.1000 0.98 5983 144 0.2485 0.2535
REMARK 3 24 2.1000 - 2.0700 0.97 5892 139 0.2519 0.2917
REMARK 3 25 2.0700 - 2.0400 0.98 6059 146 0.2584 0.2791
REMARK 3 26 2.0400 - 2.0200 0.98 5945 143 0.2631 0.3180
REMARK 3 27 2.0200 - 1.9900 0.72 4414 106 0.2731 0.3168
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) : 0.208
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.469
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.42
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.007 8280
REMARK 3 ANGLE : 1.115 11252
REMARK 3 CHIRALITY : 0.069 1218
REMARK 3 PLANARITY : 0.007 1418
REMARK 3 DIHEDRAL : 19.280 3129
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 296 )
REMARK 3 ORIGIN FOR THE GROUP (A): 43.8144 -21.4893 52.7591
REMARK 3 T TENSOR
REMARK 3 T11: 0.4067 T22: 0.2718
REMARK 3 T33: 0.3264 T12: 0.0031
REMARK 3 T13: 0.0017 T23: 0.0598
REMARK 3 L TENSOR
REMARK 3 L11: 0.3666 L22: 0.1794
REMARK 3 L33: 1.0282 L12: 0.1090
REMARK 3 L13: 0.0684 L23: 0.3235
REMARK 3 S TENSOR
REMARK 3 S11: 0.1255 S12: -0.1431 S13: -0.1621
REMARK 3 S21: 0.1654 S22: 0.0620 S23: 0.0842
REMARK 3 S31: 0.1522 S32: -0.0719 S33: 0.0012
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 297 THROUGH 554 )
REMARK 3 ORIGIN FOR THE GROUP (A): 24.1676 -3.6031 11.7490
REMARK 3 T TENSOR
REMARK 3 T11: 0.2327 T22: 0.3057
REMARK 3 T33: 0.3205 T12: 0.0102
REMARK 3 T13: 0.0343 T23: -0.0011
REMARK 3 L TENSOR
REMARK 3 L11: 0.9055 L22: 0.2144
REMARK 3 L33: 0.5664 L12: -0.4672
REMARK 3 L13: 0.8096 L23: -0.3480
REMARK 3 S TENSOR
REMARK 3 S11: 0.0183 S12: -0.0549 S13: -0.1420
REMARK 3 S21: 0.0312 S22: 0.0922 S23: 0.1141
REMARK 3 S31: 0.0635 S32: -0.1502 S33: 0.0001
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 5 THROUGH 83 )
REMARK 3 ORIGIN FOR THE GROUP (A): 56.3046 1.4135 36.6947
REMARK 3 T TENSOR
REMARK 3 T11: 0.3414 T22: 0.3583
REMARK 3 T33: 0.2832 T12: -0.0379
REMARK 3 T13: -0.0130 T23: 0.0075
REMARK 3 L TENSOR
REMARK 3 L11: 0.4393 L22: 0.5133
REMARK 3 L33: 0.3650 L12: -0.0148
REMARK 3 L13: 0.2370 L23: -0.1870
REMARK 3 S TENSOR
REMARK 3 S11: -0.0019 S12: 0.0505 S13: -0.0593
REMARK 3 S21: 0.2132 S22: -0.0788 S23: 0.0301
REMARK 3 S31: -0.0933 S32: 0.2054 S33: -0.0006
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 84 THROUGH 194 )
REMARK 3 ORIGIN FOR THE GROUP (A): 61.0435 14.9629 34.3667
REMARK 3 T TENSOR
REMARK 3 T11: 0.4042 T22: 0.3423
REMARK 3 T33: 0.3735 T12: -0.2157
REMARK 3 T13: -0.1415 T23: 0.0920
REMARK 3 L TENSOR
REMARK 3 L11: 0.8849 L22: 0.7336
REMARK 3 L33: 0.5613 L12: -0.5695
REMARK 3 L13: 0.4822 L23: 0.0519
REMARK 3 S TENSOR
REMARK 3 S11: -0.1988 S12: 0.1517 S13: 0.3225
REMARK 3 S21: 0.2979 S22: -0.0083 S23: -0.2041
REMARK 3 S31: -0.1407 S32: 0.3802 S33: -0.1082
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 195 THROUGH 269 )
REMARK 3 ORIGIN FOR THE GROUP (A): 52.1520 20.6831 12.9227
REMARK 3 T TENSOR
REMARK 3 T11: 0.1725 T22: 0.5904
REMARK 3 T33: 0.4329 T12: -0.1777
REMARK 3 T13: 0.0508 T23: 0.1247
REMARK 3 L TENSOR
REMARK 3 L11: 0.3495 L22: 0.5164
REMARK 3 L33: 0.5916 L12: 0.2808
REMARK 3 L13: 0.0830 L23: 0.0516
REMARK 3 S TENSOR
REMARK 3 S11: -0.0383 S12: 0.0346 S13: -0.0596
REMARK 3 S21: -0.0040 S22: -0.1313 S23: -0.3080
REMARK 3 S31: -0.2785 S32: 0.4183 S33: -0.3885
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 270 THROUGH 428 )
REMARK 3 ORIGIN FOR THE GROUP (A): 37.6455 18.6236 13.9583
REMARK 3 T TENSOR
REMARK 3 T11: 0.2986 T22: 0.2667
REMARK 3 T33: 0.2641 T12: -0.0153
REMARK 3 T13: 0.0190 T23: -0.0313
REMARK 3 L TENSOR
REMARK 3 L11: 0.6858 L22: 0.8145
REMARK 3 L33: 0.8011 L12: 0.2473
REMARK 3 L13: 0.4757 L23: -0.4616
REMARK 3 S TENSOR
REMARK 3 S11: -0.0594 S12: 0.0666 S13: 0.0636
REMARK 3 S21: 0.1788 S22: -0.0611 S23: 0.0413
REMARK 3 S31: -0.1426 S32: 0.0530 S33: 0.0000
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 8DXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-22.
REMARK 100 THE DEPOSITION ID IS D_1000267496.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-APR-19
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.4-6.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 23-ID-D
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 : 85462
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 3.700
REMARK 200 R MERGE (I) : 0.05400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.70
REMARK 200 R MERGE FOR SHELL (I) : 0.47100
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: PHENIX
REMARK 200 STARTING MODEL: 4G1Q
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.01
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10-12% PEG 8000, 4% PEG 400, 100 MM
REMARK 280 IMIDAZOLE PH 6.4-6.6, 15 MM MGSO4, 100 MM AMM SULFATE, 5 MM TCEP,
REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 81.25600
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.48450
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 81.25600
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.48450
REMARK 290 SMTRY3 4 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: 8250 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 46010 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 555
REMARK 465 PRO B 1
REMARK 465 ILE B 2
REMARK 465 SER B 3
REMARK 465 PRO B 4
REMARK 465 THR B 215
REMARK 465 THR B 216
REMARK 465 PRO B 217
REMARK 465 ASP B 218
REMARK 465 LYS B 219
REMARK 465 LYS B 220
REMARK 465 HIS B 221
REMARK 465 GLN B 222
REMARK 465 LYS B 223
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 GLU B 224 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 ASP A 121 119.80 -37.99
REMARK 500 MET A 184 -126.90 55.06
REMARK 500 ILE A 270 -23.40 -144.79
REMARK 500 LYS A 287 44.06 -143.42
REMARK 500 GLU A 413 126.17 -39.65
REMARK 500 GLN B 85 159.28 -47.17
REMARK 500 GLU B 89 -71.20 -58.76
REMARK 500 MET B 184 -120.68 50.45
REMARK 500 LYS B 347 67.80 -118.25
REMARK 500 ALA B 355 -21.28 -156.25
REMARK 500 ARG B 356 40.62 -80.08
REMARK 500 ALA B 360 36.41 -151.45
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 A 607 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 443 OD2
REMARK 620 2 ASP A 549 OD1 75.5
REMARK 620 3 HOH A 710 O 70.8 80.7
REMARK 620 4 HOH A 772 O 101.6 174.7 102.7
REMARK 620 5 HOH A 859 O 83.3 84.0 152.5 91.3
REMARK 620 6 HOH A 865 O 161.0 88.2 116.7 93.9 85.4
REMARK 620 N 1 2 3 4 5
DBREF 8DXM A 1 555 UNP P03366 POL_HV1B1 600 1154
DBREF 8DXM B 1 428 UNP P03366 POL_HV1B1 600 1027
SEQADV 8DXM MET A -1 UNP P03366 EXPRESSION TAG
SEQADV 8DXM VAL A 0 UNP P03366 EXPRESSION TAG
SEQADV 8DXM ALA A 172 UNP P03366 LYS 771 ENGINEERED MUTATION
SEQADV 8DXM ALA A 173 UNP P03366 LYS 772 ENGINEERED MUTATION
SEQADV 8DXM SER A 280 UNP P03366 CYS 879 ENGINEERED MUTATION
SEQADV 8DXM SER B 280 UNP P03366 CYS 879 ENGINEERED MUTATION
SEQRES 1 A 557 MET VAL PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS
SEQRES 2 A 557 LEU LYS PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP
SEQRES 3 A 557 PRO LEU THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE
SEQRES 4 A 557 CYS THR GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE
SEQRES 5 A 557 GLY PRO GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE
SEQRES 6 A 557 LYS LYS LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP
SEQRES 7 A 557 PHE ARG GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU
SEQRES 8 A 557 VAL GLN LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS
SEQRES 9 A 557 LYS LYS SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR
SEQRES 10 A 557 PHE SER VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR
SEQRES 11 A 557 ALA PHE THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY
SEQRES 12 A 557 ILE ARG TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS
SEQRES 13 A 557 GLY SER PRO ALA ILE PHE GLN SER SER MET THR LYS ILE
SEQRES 14 A 557 LEU GLU PRO PHE ALA ALA GLN ASN PRO ASP ILE VAL ILE
SEQRES 15 A 557 TYR GLN TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU
SEQRES 16 A 557 GLU ILE GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG
SEQRES 17 A 557 GLN HIS LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS
SEQRES 18 A 557 LYS HIS GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR
SEQRES 19 A 557 GLU LEU HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL
SEQRES 20 A 557 LEU PRO GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN
SEQRES 21 A 557 LYS LEU VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR
SEQRES 22 A 557 PRO GLY ILE LYS VAL ARG GLN LEU SER LYS LEU LEU ARG
SEQRES 23 A 557 GLY THR LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU
SEQRES 24 A 557 GLU ALA GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU
SEQRES 25 A 557 LYS GLU PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS
SEQRES 26 A 557 ASP LEU ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN
SEQRES 27 A 557 TRP THR TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU
SEQRES 28 A 557 LYS THR GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR
SEQRES 29 A 557 ASN ASP VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE
SEQRES 30 A 557 THR THR GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS
SEQRES 31 A 557 PHE LYS LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP
SEQRES 32 A 557 TRP THR GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP
SEQRES 33 A 557 GLU PHE VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR
SEQRES 34 A 557 GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE
SEQRES 35 A 557 TYR VAL ASP GLY ALA ALA ASN ARG GLU THR LYS LEU GLY
SEQRES 36 A 557 LYS ALA GLY TYR VAL THR ASN LYS GLY ARG GLN LYS VAL
SEQRES 37 A 557 VAL PRO LEU THR ASN THR THR ASN GLN LYS THR GLU LEU
SEQRES 38 A 557 GLN ALA ILE TYR LEU ALA LEU GLN ASP SER GLY LEU GLU
SEQRES 39 A 557 VAL ASN ILE VAL THR ASP SER GLN TYR ALA LEU GLY ILE
SEQRES 40 A 557 ILE GLN ALA GLN PRO ASP LYS SER GLU SER GLU LEU VAL
SEQRES 41 A 557 ASN GLN ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS VAL
SEQRES 42 A 557 TYR LEU ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY GLY
SEQRES 43 A 557 ASN GLU GLN VAL ASP LYS LEU VAL SER ALA GLY
SEQRES 1 B 428 PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS LEU LYS
SEQRES 2 B 428 PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP PRO LEU
SEQRES 3 B 428 THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE CYS THR
SEQRES 4 B 428 GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE GLY PRO
SEQRES 5 B 428 GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE LYS LYS
SEQRES 6 B 428 LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP PHE ARG
SEQRES 7 B 428 GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU VAL GLN
SEQRES 8 B 428 LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS LYS LYS
SEQRES 9 B 428 SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR PHE SER
SEQRES 10 B 428 VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR ALA PHE
SEQRES 11 B 428 THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY ILE ARG
SEQRES 12 B 428 TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS GLY SER
SEQRES 13 B 428 PRO ALA ILE PHE GLN SER SER MET THR LYS ILE LEU GLU
SEQRES 14 B 428 PRO PHE LYS LYS GLN ASN PRO ASP ILE VAL ILE TYR GLN
SEQRES 15 B 428 TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU GLU ILE
SEQRES 16 B 428 GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG GLN HIS
SEQRES 17 B 428 LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS LYS HIS
SEQRES 18 B 428 GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR GLU LEU
SEQRES 19 B 428 HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL LEU PRO
SEQRES 20 B 428 GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN LYS LEU
SEQRES 21 B 428 VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR PRO GLY
SEQRES 22 B 428 ILE LYS VAL ARG GLN LEU SER LYS LEU LEU ARG GLY THR
SEQRES 23 B 428 LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU GLU ALA
SEQRES 24 B 428 GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU LYS GLU
SEQRES 25 B 428 PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS ASP LEU
SEQRES 26 B 428 ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN TRP THR
SEQRES 27 B 428 TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU LYS THR
SEQRES 28 B 428 GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR ASN ASP
SEQRES 29 B 428 VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE THR THR
SEQRES 30 B 428 GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS PHE LYS
SEQRES 31 B 428 LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP TRP THR
SEQRES 32 B 428 GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP GLU PHE
SEQRES 33 B 428 VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR GLN
HET BML A 601 8
HET T27 A 602 28
HET DMS A 603 4
HET DMS A 604 4
HET DMS A 605 4
HET DMS A 606 4
HET MG A 607 1
HET SO4 A 608 5
HET SO4 A 609 5
HET SO4 A 610 5
HET DMS B 501 4
HET DMS B 502 4
HET DMS B 503 4
HET DMS B 504 4
HET DMS B 505 4
HET EDO B 506 4
HETNAM BML 4-BROMOPHENOL
HETNAM T27 4-{[4-({4-[(E)-2-CYANOETHENYL]-2,6-
HETNAM 2 T27 DIMETHYLPHENYL}AMINO)PYRIMIDIN-2-YL]AMINO}BENZONITRILE
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM MG MAGNESIUM ION
HETNAM SO4 SULFATE ION
HETNAM EDO 1,2-ETHANEDIOL
HETSYN T27 RILPIVIRINE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 3 BML C6 H5 BR O
FORMUL 4 T27 C22 H18 N6
FORMUL 5 DMS 9(C2 H6 O S)
FORMUL 9 MG MG 2+
FORMUL 10 SO4 3(O4 S 2-)
FORMUL 18 EDO C2 H6 O2
FORMUL 19 HOH *485(H2 O)
HELIX 1 AA1 THR A 27 GLU A 44 1 18
HELIX 2 AA2 PHE A 77 THR A 84 1 8
HELIX 3 AA3 GLU A 89 GLY A 93 5 5
HELIX 4 AA4 HIS A 96 LEU A 100 5 5
HELIX 5 AA5 VAL A 111 PHE A 116 1 6
HELIX 6 AA6 ASP A 121 ALA A 129 5 9
HELIX 7 AA7 SER A 134 GLU A 138 5 5
HELIX 8 AA8 GLY A 155 ASN A 175 1 21
HELIX 9 AA9 GLU A 194 ARG A 211 1 18
HELIX 10 AB1 THR A 253 SER A 268 1 16
HELIX 11 AB2 VAL A 276 LEU A 282 1 7
HELIX 12 AB3 THR A 296 LEU A 310 1 15
HELIX 13 AB4 ASN A 363 GLY A 384 1 22
HELIX 14 AB5 GLN A 394 TYR A 405 1 12
HELIX 15 AB6 THR A 473 SER A 489 1 17
HELIX 16 AB7 SER A 499 GLN A 507 1 9
HELIX 17 AB8 SER A 515 LYS A 528 1 14
HELIX 18 AB9 GLY A 544 ALA A 554 1 11
HELIX 19 AC1 THR B 27 GLU B 44 1 18
HELIX 20 AC2 PHE B 77 THR B 84 1 8
HELIX 21 AC3 GLY B 99 LYS B 103 5 5
HELIX 22 AC4 GLY B 112 VAL B 118 5 7
HELIX 23 AC5 PHE B 124 ALA B 129 5 6
HELIX 24 AC6 SER B 134 GLU B 138 5 5
HELIX 25 AC7 LYS B 154 ASN B 175 1 22
HELIX 26 AC8 GLU B 194 LEU B 214 1 21
HELIX 27 AC9 HIS B 235 TRP B 239 5 5
HELIX 28 AD1 VAL B 254 SER B 268 1 15
HELIX 29 AD2 VAL B 276 LYS B 281 1 6
HELIX 30 AD3 LEU B 282 ARG B 284 5 3
HELIX 31 AD4 THR B 296 LYS B 311 1 16
HELIX 32 AD5 ASN B 363 GLY B 384 1 22
HELIX 33 AD6 GLN B 394 TRP B 402 1 9
HELIX 34 AD7 THR B 403 TYR B 405 5 3
HELIX 35 AD8 VAL B 423 GLN B 428 1 6
SHEET 1 AA1 3 ILE A 47 LYS A 49 0
SHEET 2 AA1 3 ILE A 142 TYR A 146 -1 O GLN A 145 N SER A 48
SHEET 3 AA1 3 PHE A 130 ILE A 132 -1 N ILE A 132 O ILE A 142
SHEET 1 AA2 2 VAL A 60 LYS A 64 0
SHEET 2 AA2 2 TRP A 71 VAL A 75 -1 O ARG A 72 N ILE A 63
SHEET 1 AA3 3 SER A 105 ASP A 110 0
SHEET 2 AA3 3 ASP A 186 SER A 191 -1 O VAL A 189 N THR A 107
SHEET 3 AA3 3 ILE A 178 TYR A 183 -1 N TYR A 181 O TYR A 188
SHEET 1 AA4 3 PHE A 227 TRP A 229 0
SHEET 2 AA4 3 TYR A 232 LEU A 234 -1 O LEU A 234 N PHE A 227
SHEET 3 AA4 3 TRP A 239 VAL A 241 -1 O THR A 240 N GLU A 233
SHEET 1 AA5 5 LYS A 347 ALA A 355 0
SHEET 2 AA5 5 GLN A 336 GLU A 344 -1 N ILE A 341 O LEU A 349
SHEET 3 AA5 5 ILE A 326 GLY A 333 -1 N ILE A 326 O TYR A 342
SHEET 4 AA5 5 LYS A 388 LEU A 391 1 O LYS A 388 N ALA A 327
SHEET 5 AA5 5 TRP A 414 PHE A 416 1 O GLU A 415 N PHE A 389
SHEET 1 AA6 2 HIS A 361 THR A 362 0
SHEET 2 AA6 2 LYS A 512 SER A 513 -1 O LYS A 512 N THR A 362
SHEET 1 AA7 5 GLN A 464 LEU A 469 0
SHEET 2 AA7 5 GLY A 453 THR A 459 -1 N ALA A 455 O VAL A 467
SHEET 3 AA7 5 THR A 439 ALA A 446 -1 N TYR A 441 O VAL A 458
SHEET 4 AA7 5 GLU A 492 THR A 497 1 O ASN A 494 N PHE A 440
SHEET 5 AA7 5 LYS A 530 TRP A 535 1 O ALA A 534 N ILE A 495
SHEET 1 AA8 3 ILE B 47 LYS B 49 0
SHEET 2 AA8 3 ILE B 142 TYR B 146 -1 O GLN B 145 N SER B 48
SHEET 3 AA8 3 PHE B 130 ILE B 132 -1 N ILE B 132 O ILE B 142
SHEET 1 AA9 2 VAL B 60 ILE B 63 0
SHEET 2 AA9 2 ARG B 72 VAL B 75 -1 O ARG B 72 N ILE B 63
SHEET 1 AB1 4 VAL B 179 TYR B 183 0
SHEET 2 AB1 4 ASP B 186 SER B 191 -1 O TYR B 188 N TYR B 181
SHEET 3 AB1 4 SER B 105 ASP B 110 -1 N LEU B 109 O LEU B 187
SHEET 4 AB1 4 TYR B 232 LEU B 234 -1 O LEU B 234 N VAL B 106
SHEET 1 AB2 2 TRP B 252 THR B 253 0
SHEET 2 AB2 2 VAL B 292 ILE B 293 -1 O ILE B 293 N TRP B 252
SHEET 1 AB3 5 ASN B 348 TYR B 354 0
SHEET 2 AB3 5 GLN B 336 TYR B 342 -1 N ILE B 341 O LYS B 350
SHEET 3 AB3 5 ILE B 326 GLY B 333 -1 N ILE B 326 O TYR B 342
SHEET 4 AB3 5 LYS B 388 LEU B 391 1 O LYS B 390 N ALA B 327
SHEET 5 AB3 5 GLU B 413 PHE B 416 1 O GLU B 415 N LEU B 391
LINK OD2 ASP A 443 MG MG A 607 1555 1555 2.52
LINK OD1 ASP A 549 MG MG A 607 1555 1555 2.46
LINK MG MG A 607 O HOH A 710 1555 1555 2.21
LINK MG MG A 607 O HOH A 772 1555 1555 2.34
LINK MG MG A 607 O HOH A 859 1555 1555 1.95
LINK MG MG A 607 O HOH A 865 1555 1555 2.07
CISPEP 1 PRO A 225 PRO A 226 0 1.69
CISPEP 2 PRO A 420 PRO A 421 0 1.08
CRYST1 162.512 72.969 109.422 90.00 100.60 90.00 C 1 2 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 0.006153 0.000000 0.001151 0.00000
SCALE2 0.000000 0.013704 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009297 0.00000