HEADER TRANSFERASE/TRANSFERASE INHIBITOR 27-JAN-11 3QIP TITLE STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH AN RNASE H TITLE 2 INHIBITOR AND NEVIRAPINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: REVERSE HIV-1 REVERSE TRANSCRIPTASE P66; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: P66 SUBUNIT (UNP RESIDUES 588-1147); COMPND 5 SYNONYM: PR160GAG-POL, MATRIX PROTEIN P17, MA, CAPSID PROTEIN P24, COMPND 6 CA, SPACER PEPTIDE P2, NUCLEOCAPSID PROTEIN P7, NC, TRANSFRAME COMPND 7 PEPTIDE, TF, P6-POL, P6*, PROTEASE, PR, RETROPEPSIN, REVERSE COMPND 8 TRANSCRIPTASE/RIBONUCLEASE H, P66 RT, P51 RT, P15, INTEGRASE, IN; COMPND 9 EC: 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: P51; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: P51 SUBUNIT (UNP RESIDUES 588-1027); COMPND 15 SYNONYM: PR160GAG-POL, MATRIX PROTEIN P17, MA, CAPSID PROTEIN P24, COMPND 16 CA, SPACER PEPTIDE P2, NUCLEOCAPSID PROTEIN P7, NC, TRANSFRAME COMPND 17 PEPTIDE, TF, P6-POL, P6*, PROTEASE, PR, RETROPEPSIN, REVERSE COMPND 18 TRANSCRIPTASE/RIBONUCLEASE H, P66 RT, P51 RT, P15, INTEGRASE, IN; COMPND 19 EC: 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HIV-1 M:B_HXB2R; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11706; SOURCE 5 GENE: GAG-POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET14B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HIV-1 M:B_HXB2R; SOURCE 13 ORGANISM_COMMON: HIV-1; SOURCE 14 ORGANISM_TAXID: 11706; SOURCE 15 GENE: GAG-POL; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET 14B KEYWDS HIV, REVERSE TRANSCRIPTASE, RNASE H, POLYMERASE, NUCLEASE, KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.B.LANSDON,T.A.KIRSCHBERG REVDAT 3 13-SEP-23 3QIP 1 REMARK LINK REVDAT 2 01-JUN-11 3QIP 1 JRNL REVDAT 1 20-APR-11 3QIP 0 JRNL AUTH E.B.LANSDON,Q.LIU,S.A.LEAVITT,M.BALAKRISHNAN,J.K.PERRY, JRNL AUTH 2 C.LANCASTER-MOYER,N.KUTTY,X.LIU,N.H.SQUIRES,W.J.WATKINS, JRNL AUTH 3 T.A.KIRSCHBERG JRNL TITL STRUCTURAL AND BINDING ANALYSIS OF PYRIMIDINOL CARBOXYLIC JRNL TITL 2 ACID AND N-HYDROXY QUINAZOLINEDIONE HIV-1 RNASE H JRNL TITL 3 INHIBITORS. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 55 2905 2011 JRNL REFN ISSN 0066-4804 JRNL PMID 21464257 JRNL DOI 10.1128/AAC.01594-10 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 76324 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3822 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 47.3663 - 6.2732 0.99 3077 172 0.1949 0.2221 REMARK 3 2 6.2732 - 4.9810 1.00 3027 128 0.2050 0.2322 REMARK 3 3 4.9810 - 4.3518 1.00 2976 142 0.1723 0.2140 REMARK 3 4 4.3518 - 3.9542 0.99 2952 140 0.1844 0.2419 REMARK 3 5 3.9542 - 3.6709 0.99 2929 158 0.1956 0.2402 REMARK 3 6 3.6709 - 3.4545 0.99 2896 156 0.2103 0.2827 REMARK 3 7 3.4545 - 3.2815 0.98 2888 160 0.2161 0.2424 REMARK 3 8 3.2815 - 3.1387 0.98 2858 140 0.2247 0.2598 REMARK 3 9 3.1387 - 3.0179 0.97 2857 145 0.2341 0.2988 REMARK 3 10 3.0179 - 2.9138 0.96 2842 145 0.2353 0.2981 REMARK 3 11 2.9138 - 2.8227 0.96 2800 155 0.2431 0.2865 REMARK 3 12 2.8227 - 2.7420 0.95 2755 160 0.2433 0.3047 REMARK 3 13 2.7420 - 2.6698 0.94 2718 143 0.2513 0.3562 REMARK 3 14 2.6698 - 2.6047 0.92 2688 145 0.2547 0.3157 REMARK 3 15 2.6047 - 2.5455 0.93 2710 149 0.2509 0.3158 REMARK 3 16 2.5455 - 2.4913 0.91 2647 137 0.2620 0.3454 REMARK 3 17 2.4913 - 2.4415 0.90 2617 150 0.2658 0.3108 REMARK 3 18 2.4415 - 2.3954 0.90 2599 134 0.2706 0.3353 REMARK 3 19 2.3954 - 2.3526 0.89 2600 147 0.2610 0.3190 REMARK 3 20 2.3526 - 2.3128 0.89 2559 150 0.2646 0.3272 REMARK 3 21 2.3128 - 2.2755 0.87 2505 160 0.2543 0.3261 REMARK 3 22 2.2755 - 2.2405 0.86 2493 132 0.2499 0.2948 REMARK 3 23 2.2405 - 2.2075 0.88 2559 131 0.2600 0.3201 REMARK 3 24 2.2075 - 2.1764 0.84 2411 127 0.2667 0.3583 REMARK 3 25 2.1764 - 2.1470 0.81 2379 115 0.2738 0.3380 REMARK 3 26 2.1470 - 2.1191 0.77 2183 135 0.2785 0.3405 REMARK 3 27 2.1191 - 2.0926 0.67 1977 66 0.2783 0.3711 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 60.51 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.39420 REMARK 3 B22 (A**2) : -9.07110 REMARK 3 B33 (A**2) : 14.46520 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.008 8110 REMARK 3 ANGLE : 1.091 11026 REMARK 3 CHIRALITY : 0.071 1191 REMARK 3 PLANARITY : 0.005 1383 REMARK 3 DIHEDRAL : 16.215 3069 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 3QIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063694. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82059 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.093 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1VRT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3M (NH4)2SO4, 5MM SODIUM MALONATE, REMARK 280 AND 100MM CACODYLATE PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 76.53950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.53950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 59.44900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 77.43800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 59.44900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 77.43800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 76.53950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.44900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 77.43800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 76.53950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 59.44900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 77.43800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 6610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 83830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -176.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 76.53950 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 770 LIES ON A SPECIAL POSITION. 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 LYS A 66 REMARK 465 ASP A 67 REMARK 465 ARG A 557 REMARK 465 LYS A 558 REMARK 465 VAL A 559 REMARK 465 LEU A 560 REMARK 465 PRO B 1 REMARK 465 ILE B 2 REMARK 465 SER B 3 REMARK 465 PRO B 4 REMARK 465 ILE B 5 REMARK 465 LYS B 66 REMARK 465 ASP B 67 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 465 GLU B 224 REMARK 465 PRO B 225 REMARK 465 PRO B 226 REMARK 465 PHE B 227 REMARK 465 LEU B 228 REMARK 465 TRP B 229 REMARK 465 MET B 230 REMARK 465 GLY B 231 REMARK 465 MET B 357 REMARK 465 ARG B 358 REMARK 465 GLY B 359 REMARK 465 ALA B 360 REMARK 465 HIS B 361 REMARK 465 LYS B 431 REMARK 465 GLU B 432 REMARK 465 PRO B 433 REMARK 465 ILE B 434 REMARK 465 VAL B 435 REMARK 465 GLY B 436 REMARK 465 ALA B 437 REMARK 465 GLU B 438 REMARK 465 THR B 439 REMARK 465 PHE B 440 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 GLY A 543 NE2 GLN A 547 2.16 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 LYS A 20 59.53 -146.88 REMARK 500 ASN A 54 109.33 -52.60 REMARK 500 ASP A 121 115.70 -39.58 REMARK 500 MET A 184 -125.95 49.47 REMARK 500 ILE A 270 -27.31 -140.14 REMARK 500 LYS A 287 -80.07 -109.86 REMARK 500 PHE A 346 61.86 -115.74 REMARK 500 ALA A 355 56.81 -147.59 REMARK 500 LYS A 465 146.56 -173.26 REMARK 500 ASP A 471 65.56 67.73 REMARK 500 MET B 184 -122.15 51.75 REMARK 500 ASP B 237 8.19 -65.88 REMARK 500 ILE B 270 -53.78 -122.06 REMARK 500 LEU B 283 49.94 -88.35 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 MN A 562 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 443 OD2 REMARK 620 2 GLU A 478 OE2 89.1 REMARK 620 3 ASP A 498 OD2 95.2 117.7 REMARK 620 4 P4Y A 900 O27 172.5 85.5 82.8 REMARK 620 5 P4Y A 900 O24 107.8 127.7 109.7 79.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 563 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 443 OD1 REMARK 620 2 ASP A 549 OD1 106.0 REMARK 620 3 HOH A 567 O 93.7 113.1 REMARK 620 4 HOH A 568 O 85.4 76.3 170.3 REMARK 620 5 P4Y A 900 O24 94.4 141.6 97.2 73.3 REMARK 620 6 P4Y A 900 O25 153.3 86.8 102.9 74.7 63.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NVP A 561 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 562 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 563 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 564 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 565 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 566 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P4Y A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 441 DBREF 3QIP A 1 560 UNP P04585 POL_HV1H2 588 1147 DBREF 3QIP B 1 440 UNP P04585 POL_HV1H2 588 1027 SEQRES 1 A 560 PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS LEU LYS SEQRES 2 A 560 PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP PRO LEU SEQRES 3 A 560 THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE CYS THR SEQRES 4 A 560 GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE GLY PRO SEQRES 5 A 560 GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE LYS LYS SEQRES 6 A 560 LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP PHE ARG SEQRES 7 A 560 GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU VAL GLN SEQRES 8 A 560 LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS LYS LYS SEQRES 9 A 560 SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR PHE SER SEQRES 10 A 560 VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR ALA PHE SEQRES 11 A 560 THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY ILE ARG SEQRES 12 A 560 TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS GLY SER SEQRES 13 A 560 PRO ALA ILE PHE GLN SER SER MET THR LYS ILE LEU GLU SEQRES 14 A 560 PRO PHE ARG LYS GLN ASN PRO ASP ILE VAL ILE TYR GLN SEQRES 15 A 560 TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU GLU ILE SEQRES 16 A 560 GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG GLN HIS SEQRES 17 A 560 LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS LYS HIS SEQRES 18 A 560 GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR GLU LEU SEQRES 19 A 560 HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL LEU PRO SEQRES 20 A 560 GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN LYS LEU SEQRES 21 A 560 VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR PRO GLY SEQRES 22 A 560 ILE LYS VAL ARG GLN LEU CYS LYS LEU LEU ARG GLY THR SEQRES 23 A 560 LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU GLU ALA SEQRES 24 A 560 GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU LYS GLU SEQRES 25 A 560 PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS ASP LEU SEQRES 26 A 560 ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN TRP THR SEQRES 27 A 560 TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU LYS THR SEQRES 28 A 560 GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR ASN ASP SEQRES 29 A 560 VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE THR THR SEQRES 30 A 560 GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS PHE LYS SEQRES 31 A 560 LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP TRP THR SEQRES 32 A 560 GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP GLU PHE SEQRES 33 A 560 VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR GLN LEU SEQRES 34 A 560 GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE TYR VAL SEQRES 35 A 560 ASP GLY ALA ALA ASN ARG GLU THR LYS LEU GLY LYS ALA SEQRES 36 A 560 GLY TYR VAL THR ASN ARG GLY ARG GLN LYS VAL VAL THR SEQRES 37 A 560 LEU THR ASP THR THR ASN GLN LYS THR GLU LEU GLN ALA SEQRES 38 A 560 ILE TYR LEU ALA LEU GLN ASP SER GLY LEU GLU VAL ASN SEQRES 39 A 560 ILE VAL THR ASP SER GLN TYR ALA LEU GLY ILE ILE GLN SEQRES 40 A 560 ALA GLN PRO ASP GLN SER GLU SER GLU LEU VAL ASN GLN SEQRES 41 A 560 ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS VAL TYR LEU SEQRES 42 A 560 ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY GLY ASN GLU SEQRES 43 A 560 GLN VAL ASP LYS LEU VAL SER ALA GLY ILE ARG LYS VAL SEQRES 44 A 560 LEU SEQRES 1 B 440 PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS LEU LYS SEQRES 2 B 440 PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP PRO LEU SEQRES 3 B 440 THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE CYS THR SEQRES 4 B 440 GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE GLY PRO SEQRES 5 B 440 GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE LYS LYS SEQRES 6 B 440 LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP PHE ARG SEQRES 7 B 440 GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU VAL GLN SEQRES 8 B 440 LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS LYS LYS SEQRES 9 B 440 SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR PHE SER SEQRES 10 B 440 VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR ALA PHE SEQRES 11 B 440 THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY ILE ARG SEQRES 12 B 440 TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS GLY SER SEQRES 13 B 440 PRO ALA ILE PHE GLN SER SER MET THR LYS ILE LEU GLU SEQRES 14 B 440 PRO PHE ARG LYS GLN ASN PRO ASP ILE VAL ILE TYR GLN SEQRES 15 B 440 TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU GLU ILE SEQRES 16 B 440 GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG GLN HIS SEQRES 17 B 440 LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS LYS HIS SEQRES 18 B 440 GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR GLU LEU SEQRES 19 B 440 HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL LEU PRO SEQRES 20 B 440 GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN LYS LEU SEQRES 21 B 440 VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR PRO GLY SEQRES 22 B 440 ILE LYS VAL ARG GLN LEU CYS LYS LEU LEU ARG GLY THR SEQRES 23 B 440 LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU GLU ALA SEQRES 24 B 440 GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU LYS GLU SEQRES 25 B 440 PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS ASP LEU SEQRES 26 B 440 ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN TRP THR SEQRES 27 B 440 TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU LYS THR SEQRES 28 B 440 GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR ASN ASP SEQRES 29 B 440 VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE THR THR SEQRES 30 B 440 GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS PHE LYS SEQRES 31 B 440 LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP TRP THR SEQRES 32 B 440 GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP GLU PHE SEQRES 33 B 440 VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR GLN LEU SEQRES 34 B 440 GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE HET NVP A 561 20 HET MN A 562 1 HET MN A 563 1 HET SO4 A 564 5 HET SO4 A 565 5 HET CL A 566 1 HET P4Y A 900 27 HET CL B 441 1 HETNAM NVP 11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2- HETNAM 2 NVP B:2',3'-E][1,4]DIAZEPIN-6-ONE HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM P4Y 5,6-DIHYDROXY-2-[(2-PHENYL-1H-INDOL-3-YL) HETNAM 2 P4Y METHYL]PYRIMIDINE-4-CARBOXYLIC ACID HETSYN NVP NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE FORMUL 3 NVP C15 H14 N4 O FORMUL 4 MN 2(MN 2+) FORMUL 6 SO4 2(O4 S 2-) FORMUL 8 CL 2(CL 1-) FORMUL 9 P4Y C20 H15 N3 O4 FORMUL 11 HOH *418(H2 O) HELIX 1 1 THR A 27 GLU A 44 1 18 HELIX 2 2 PHE A 77 THR A 84 1 8 HELIX 3 3 HIS A 96 LEU A 100 5 5 HELIX 4 4 ALA A 114 VAL A 118 5 5 HELIX 5 5 ASP A 121 ALA A 129 5 9 HELIX 6 6 SER A 134 GLU A 138 5 5 HELIX 7 7 GLY A 155 ASN A 175 1 21 HELIX 8 8 GLU A 194 TRP A 212 1 19 HELIX 9 9 ASP A 218 GLN A 222 5 5 HELIX 10 10 THR A 253 SER A 268 1 16 HELIX 11 11 VAL A 276 LEU A 283 1 8 HELIX 12 12 THR A 296 LEU A 310 1 15 HELIX 13 13 ASN A 363 GLY A 384 1 22 HELIX 14 14 GLN A 394 TYR A 405 1 12 HELIX 15 15 THR A 473 ASP A 488 1 16 HELIX 16 16 SER A 499 ALA A 508 1 10 HELIX 17 17 SER A 515 LYS A 528 1 14 HELIX 18 18 ILE A 542 SER A 553 1 12 HELIX 19 19 THR B 27 GLU B 44 1 18 HELIX 20 20 PHE B 77 THR B 84 1 8 HELIX 21 21 THR B 84 VAL B 90 1 7 HELIX 22 22 GLY B 99 LYS B 103 5 5 HELIX 23 23 GLY B 112 VAL B 118 5 7 HELIX 24 24 PHE B 124 ALA B 129 5 6 HELIX 25 25 SER B 134 GLU B 138 5 5 HELIX 26 26 LYS B 154 ASN B 175 1 22 HELIX 27 27 GLU B 194 ARG B 211 1 18 HELIX 28 28 HIS B 235 TRP B 239 5 5 HELIX 29 29 THR B 253 SER B 268 1 16 HELIX 30 30 VAL B 276 LEU B 282 1 7 HELIX 31 31 THR B 296 LYS B 311 1 16 HELIX 32 32 ASN B 363 GLY B 384 1 22 HELIX 33 33 GLN B 394 TRP B 406 1 13 HELIX 34 34 PRO B 420 TYR B 427 1 8 SHEET 1 A 3 ILE A 47 LYS A 49 0 SHEET 2 A 3 ILE A 142 TYR A 146 -1 O GLN A 145 N SER A 48 SHEET 3 A 3 PHE A 130 ILE A 132 -1 N PHE A 130 O TYR A 144 SHEET 1 B 2 VAL A 60 LYS A 64 0 SHEET 2 B 2 TRP A 71 VAL A 75 -1 O LEU A 74 N PHE A 61 SHEET 1 C 3 SER A 105 ASP A 110 0 SHEET 2 C 3 ASP A 186 SER A 191 -1 O VAL A 189 N THR A 107 SHEET 3 C 3 VAL A 179 TYR A 183 -1 N TYR A 183 O ASP A 186 SHEET 1 D 3 PHE A 227 TRP A 229 0 SHEET 2 D 3 TYR A 232 LEU A 234 -1 O LEU A 234 N PHE A 227 SHEET 3 D 3 TRP A 239 VAL A 241 -1 O THR A 240 N GLU A 233 SHEET 1 E 5 ASN A 348 TYR A 354 0 SHEET 2 E 5 TRP A 337 TYR A 342 -1 N ILE A 341 O LYS A 350 SHEET 3 E 5 ILE A 326 LYS A 331 -1 N ILE A 326 O TYR A 342 SHEET 4 E 5 LYS A 388 LEU A 391 1 O LYS A 388 N ALA A 327 SHEET 5 E 5 TRP A 414 PHE A 416 1 O GLU A 415 N LEU A 391 SHEET 1 F 2 HIS A 361 THR A 362 0 SHEET 2 F 2 GLN A 512 SER A 513 -1 O GLN A 512 N THR A 362 SHEET 1 G 5 GLN A 464 THR A 470 0 SHEET 2 G 5 LEU A 452 THR A 459 -1 N GLY A 453 O LEU A 469 SHEET 3 G 5 GLU A 438 ALA A 446 -1 N TYR A 441 O VAL A 458 SHEET 4 G 5 GLU A 492 THR A 497 1 O ASN A 494 N PHE A 440 SHEET 5 G 5 LYS A 530 TRP A 535 1 O ALA A 534 N ILE A 495 SHEET 1 H 3 ILE B 47 LYS B 49 0 SHEET 2 H 3 ILE B 142 TYR B 146 -1 O GLN B 145 N SER B 48 SHEET 3 H 3 PHE B 130 ILE B 132 -1 N PHE B 130 O TYR B 144 SHEET 1 I 2 VAL B 60 ILE B 63 0 SHEET 2 I 2 ARG B 72 VAL B 75 -1 O LEU B 74 N PHE B 61 SHEET 1 J 4 VAL B 179 TYR B 183 0 SHEET 2 J 4 ASP B 186 SER B 191 -1 O TYR B 188 N TYR B 181 SHEET 3 J 4 SER B 105 ASP B 110 -1 N LEU B 109 O LEU B 187 SHEET 4 J 4 GLU B 233 LEU B 234 -1 O LEU B 234 N VAL B 106 SHEET 1 K 5 ASN B 348 ALA B 355 0 SHEET 2 K 5 GLN B 336 TYR B 342 -1 N ILE B 341 O LYS B 350 SHEET 3 K 5 ILE B 326 GLY B 333 -1 N GLN B 330 O THR B 338 SHEET 4 K 5 LYS B 388 LEU B 391 1 O LYS B 390 N ALA B 327 SHEET 5 K 5 TRP B 414 PHE B 416 1 O GLU B 415 N LEU B 391 LINK OD2 ASP A 443 MN MN A 562 1555 1555 2.09 LINK OD1 ASP A 443 MN MN A 563 1555 1555 2.30 LINK OE2 GLU A 478 MN MN A 562 1555 1555 2.16 LINK OD2 ASP A 498 MN MN A 562 1555 1555 2.34 LINK OD1 ASP A 549 MN MN A 563 1555 1555 2.31 LINK MN MN A 562 O27 P4Y A 900 1555 1555 1.76 LINK MN MN A 562 O24 P4Y A 900 1555 1555 2.22 LINK MN MN A 563 O HOH A 567 1555 1555 2.39 LINK MN MN A 563 O HOH A 568 1555 1555 2.14 LINK MN MN A 563 O24 P4Y A 900 1555 1555 2.46 LINK MN MN A 563 O25 P4Y A 900 1555 1555 2.75 CISPEP 1 PRO A 225 PRO A 226 0 -3.30 CISPEP 2 PRO A 345 PHE A 346 0 -8.65 CISPEP 3 PRO A 420 PRO A 421 0 -0.33 SITE 1 AC1 13 LEU A 100 LYS A 101 VAL A 106 VAL A 179 SITE 2 AC1 13 TYR A 181 TYR A 188 GLY A 190 PHE A 227 SITE 3 AC1 13 TRP A 229 HIS A 235 HOH A 584 HOH A 589 SITE 4 AC1 13 HOH A 632 SITE 1 AC2 4 ASP A 443 GLU A 478 ASP A 498 P4Y A 900 SITE 1 AC3 5 ASP A 443 ASP A 549 HOH A 567 HOH A 568 SITE 2 AC3 5 P4Y A 900 SITE 1 AC4 8 ARG A 211 GLY A 436 ALA A 437 GLU A 438 SITE 2 AC4 8 ASN A 460 ARG A 461 HOH A 606 ALA B 288 SITE 1 AC5 4 GLN A 207 GLY A 436 ARG A 461 HOH A 810 SITE 1 AC6 3 SER A 515 GLU A 516 HOH A 742 SITE 1 AC7 11 ASP A 443 ARG A 448 GLU A 478 ASP A 498 SITE 2 AC7 11 ALA A 538 HIS A 539 ASP A 549 MN A 562 SITE 3 AC7 11 MN A 563 HOH A 568 HOH A 771 SITE 1 AC8 1 HOH B 557 CRYST1 118.898 154.876 153.079 90.00 90.00 90.00 C 2 2 21 8 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 0.008411 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006457 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006533 0.00000