HEADER TRANSFERASE/HYDROLASE 04-FEB-10 3LP1 TITLE HIV-1 REVERSE TRANSCRIPTASE WITH INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: REVERSE TRANSCRIPTASE/RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: P66 RT; COMPND 5 EC: 2.7.7.49, 2.7.7.7, 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: P51 RT; COMPND 9 CHAIN: B; COMPND 10 EC: 2.7.7.49, 2.7.7.7; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11706; SOURCE 5 STRAIN: HXB2; SOURCE 6 GENE: GAG-POL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 12 ORGANISM_COMMON: HIV-1; SOURCE 13 ORGANISM_TAXID: 11706; SOURCE 14 STRAIN: HXB2; SOURCE 15 GENE: GAG-POL; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS REVERSE TRANSCRIPTASE, RNASE H, HIV, AIDS, CAPSID MATURATION, DNA KEYWDS 2 INTEGRATION, DNA-DIRECTED DNA POLYMERASE, ENDONUCLEASE, HOST KEYWDS 3 CYTOPLASM, HOST MEMBRANE, HOST NUCLEUS, HOST-VIRUS INTERACTION, KEYWDS 4 HYDROLASE, MAGNESIUM, MEMBRANE, METAL-BINDING, MULTIFUNCTIONAL KEYWDS 5 ENZYME, MYRISTATE, NUCLEASE, NUCLEOTIDYLTRANSFERASE, RNA-BINDING, KEYWDS 6 RNA-DIRECTED DNA POLYMERASE, TRANSFERASE, VIRAL NUCLEOPROTEIN, KEYWDS 7 VIRION, TRANSFERASE-HYDROLASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.YAN,S.K.MUNSHI,G.S.PRASAD,H.P.SU REVDAT 4 21-FEB-24 3LP1 1 REMARK SEQADV LINK REVDAT 3 01-NOV-17 3LP1 1 REMARK REVDAT 2 21-JUL-10 3LP1 1 JRNL REVDAT 1 09-JUN-10 3LP1 0 JRNL AUTH H.P.SU,Y.YAN,G.S.PRASAD,R.F.SMITH,C.L.DANIELS, JRNL AUTH 2 P.D.ABEYWICKREMA,J.C.REID,H.M.LOUGHRAN,M.KORNIENKO,S.SHARMA, JRNL AUTH 3 J.A.GROBLER,B.XU,V.SARDANA,T.J.ALLISON,P.D.WILLIAMS, JRNL AUTH 4 P.L.DARKE,D.J.HAZUDA,S.MUNSHI JRNL TITL STRUCTURAL BASIS FOR THE INHIBITION OF RNASE H ACTIVITY OF JRNL TITL 2 HIV-1 REVERSE TRANSCRIPTASE BY RNASE H ACTIVE SITE-DIRECTED JRNL TITL 3 INHIBITORS. JRNL REF J.VIROL. V. 84 7625 2010 JRNL REFN ISSN 0022-538X JRNL PMID 20484498 JRNL DOI 10.1128/JVI.00353-10 REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 64255 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.269 REMARK 3 R VALUE (WORKING SET) : 0.268 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3410 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4580 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE SET COUNT : 255 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7814 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.38000 REMARK 3 B22 (A**2) : -0.95000 REMARK 3 B33 (A**2) : 0.56000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.307 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.237 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.191 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.594 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8067 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10968 ; 0.962 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 948 ; 4.901 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 362 ;36.526 ;25.221 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1453 ;15.856 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;14.085 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1187 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6024 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3637 ; 0.168 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5456 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 313 ; 0.106 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 56 ; 0.148 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.086 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4967 ; 0.353 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7822 ; 0.628 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3697 ; 0.490 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3146 ; 0.822 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3LP1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057551. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC/MAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67667 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 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 (%) : 96.3 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.25100 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.8, 0.8 M REMARK 280 SODIUM CITRATE, SITTING DROP, TEMPERATURE 298K 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 77.62200 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 77.62200 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 59.39200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 77.63200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 59.39200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 77.63200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 77.62200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.39200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 77.63200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 77.62200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 59.39200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 77.63200 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: 6010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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: 16760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 84960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -99.0 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 77.62200 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 -2 REMARK 465 ASN A -1 REMARK 465 LYS A 65 REMARK 465 LYS A 66 REMARK 465 ASP A 67 REMARK 465 SER A 68 REMARK 465 LYS A 558 REMARK 465 VAL A 559 REMARK 465 LEU A 560 REMARK 465 MET B -2 REMARK 465 ASN B -1 REMARK 465 SER B 0 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 65 REMARK 465 LYS B 66 REMARK 465 ASP B 67 REMARK 465 SER B 68 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 MET B 357 REMARK 465 ARG B 358 REMARK 465 GLY B 359 REMARK 465 ALA B 360 REMARK 465 LEU B 429 REMARK 465 GLU B 430 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 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 SER A 0 OG REMARK 470 ARG A 557 CD NE CZ NH1 NH2 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 ASN A 136 -142.53 57.89 REMARK 500 GLU A 138 -96.31 -14.98 REMARK 500 MET A 184 -117.59 51.12 REMARK 500 ILE A 270 -24.11 -142.30 REMARK 500 LYS A 287 -150.49 -76.82 REMARK 500 PRO A 345 105.75 -30.30 REMARK 500 PHE A 346 9.27 80.83 REMARK 500 ALA A 355 -26.93 -142.13 REMARK 500 ARG A 356 135.10 -38.20 REMARK 500 GLU A 413 123.87 -32.45 REMARK 500 ASP B 17 -168.26 -113.95 REMARK 500 GLN B 91 -44.94 -156.61 REMARK 500 MET B 184 -120.04 52.91 REMARK 500 SER B 251 97.92 76.53 REMARK 500 THR B 296 -130.68 -78.22 REMARK 500 GLU B 297 -6.22 -152.31 REMARK 500 PHE B 346 -27.78 84.64 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 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 443 OD1 REMARK 620 2 ASP A 549 OD1 101.1 REMARK 620 3 LP8 A 601 O 102.8 155.9 REMARK 620 4 LP8 A 601 O3 165.7 87.3 70.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 603 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 443 OD2 REMARK 620 2 GLU A 478 OE2 105.5 REMARK 620 3 ASP A 498 OD1 95.2 110.5 REMARK 620 4 LP8 A 601 O 92.7 116.7 127.9 REMARK 620 5 LP8 A 601 N9 162.3 90.1 86.9 72.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LP8 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NVP A 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LP0 RELATED DB: PDB REMARK 900 RELATED ID: 3LP2 RELATED DB: PDB REMARK 900 RELATED ID: 3LP3 RELATED DB: PDB DBREF 3LP1 A 1 560 UNP P04585 POL_HV1H2 588 1147 DBREF 3LP1 B 1 440 UNP P04585 POL_HV1H2 588 1027 SEQADV 3LP1 MET A -2 UNP P04585 EXPRESSION TAG SEQADV 3LP1 ASN A -1 UNP P04585 EXPRESSION TAG SEQADV 3LP1 SER A 0 UNP P04585 EXPRESSION TAG SEQADV 3LP1 MET B -2 UNP P04585 EXPRESSION TAG SEQADV 3LP1 ASN B -1 UNP P04585 EXPRESSION TAG SEQADV 3LP1 SER B 0 UNP P04585 EXPRESSION TAG SEQRES 1 A 563 MET ASN SER PRO ILE SER PRO ILE GLU THR VAL PRO VAL SEQRES 2 A 563 LYS LEU LYS PRO GLY MET ASP GLY PRO LYS VAL LYS GLN SEQRES 3 A 563 TRP PRO LEU THR GLU GLU LYS ILE LYS ALA LEU VAL GLU SEQRES 4 A 563 ILE CYS THR GLU MET GLU LYS GLU GLY LYS ILE SER LYS SEQRES 5 A 563 ILE GLY PRO GLU ASN PRO TYR ASN THR PRO VAL PHE ALA SEQRES 6 A 563 ILE LYS LYS LYS ASP SER THR LYS TRP ARG LYS LEU VAL SEQRES 7 A 563 ASP PHE ARG GLU LEU ASN LYS ARG THR GLN ASP PHE TRP SEQRES 8 A 563 GLU VAL GLN LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS SEQRES 9 A 563 LYS ASN LYS SER VAL THR VAL LEU ASP VAL GLY ASP ALA SEQRES 10 A 563 TYR PHE SER VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR SEQRES 11 A 563 THR ALA PHE THR ILE PRO SER ILE ASN ASN GLU THR PRO SEQRES 12 A 563 GLY ILE ARG TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP SEQRES 13 A 563 LYS GLY SER PRO ALA ILE PHE GLN SER SER MET THR LYS SEQRES 14 A 563 ILE LEU GLU PRO PHE ARG LYS GLN ASN PRO ASP ILE VAL SEQRES 15 A 563 ILE TYR GLN TYR MET ASP ASP LEU TYR VAL GLY SER ASP SEQRES 16 A 563 LEU GLU ILE GLY GLN HIS ARG THR LYS ILE GLU GLU LEU SEQRES 17 A 563 ARG GLN HIS LEU LEU ARG TRP GLY LEU THR THR PRO ASP SEQRES 18 A 563 LYS LYS HIS GLN LYS GLU PRO PRO PHE LEU TRP MET GLY SEQRES 19 A 563 TYR GLU LEU HIS PRO ASP LYS TRP THR VAL GLN PRO ILE SEQRES 20 A 563 VAL LEU PRO GLU LYS ASP SER TRP THR VAL ASN ASP ILE SEQRES 21 A 563 GLN LYS LEU VAL GLY LYS LEU ASN TRP ALA SER GLN ILE SEQRES 22 A 563 TYR PRO GLY ILE LYS VAL ARG GLN LEU CYS LYS LEU LEU SEQRES 23 A 563 ARG GLY THR LYS ALA LEU THR GLU VAL ILE PRO LEU THR SEQRES 24 A 563 GLU GLU ALA GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE SEQRES 25 A 563 LEU LYS GLU PRO VAL HIS GLY VAL TYR TYR ASP PRO SER SEQRES 26 A 563 LYS ASP LEU ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY SEQRES 27 A 563 GLN TRP THR TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN SEQRES 28 A 563 LEU LYS THR GLY LYS TYR ALA ARG MET ARG GLY ALA HIS SEQRES 29 A 563 THR ASN ASP VAL LYS GLN LEU THR GLU ALA VAL GLN LYS SEQRES 30 A 563 ILE THR THR GLU SER ILE VAL ILE TRP GLY LYS THR PRO SEQRES 31 A 563 LYS PHE LYS LEU PRO ILE GLN LYS GLU THR TRP GLU THR SEQRES 32 A 563 TRP TRP THR GLU TYR TRP GLN ALA THR TRP ILE PRO GLU SEQRES 33 A 563 TRP GLU PHE VAL ASN THR PRO PRO LEU VAL LYS LEU TRP SEQRES 34 A 563 TYR GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA GLU THR SEQRES 35 A 563 PHE TYR VAL ASP GLY ALA ALA ASN ARG GLU THR LYS LEU SEQRES 36 A 563 GLY LYS ALA GLY TYR VAL THR ASN ARG GLY ARG GLN LYS SEQRES 37 A 563 VAL VAL THR LEU THR ASP THR THR ASN GLN LYS THR GLU SEQRES 38 A 563 LEU GLN ALA ILE TYR LEU ALA LEU GLN ASP SER GLY LEU SEQRES 39 A 563 GLU VAL ASN ILE VAL THR ASP SER GLN TYR ALA LEU GLY SEQRES 40 A 563 ILE ILE GLN ALA GLN PRO ASP GLN SER GLU SER GLU LEU SEQRES 41 A 563 VAL ASN GLN ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS SEQRES 42 A 563 VAL TYR LEU ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY SEQRES 43 A 563 GLY ASN GLU GLN VAL ASP LYS LEU VAL SER ALA GLY ILE SEQRES 44 A 563 ARG LYS VAL LEU SEQRES 1 B 443 MET ASN SER PRO ILE SER PRO ILE GLU THR VAL PRO VAL SEQRES 2 B 443 LYS LEU LYS PRO GLY MET ASP GLY PRO LYS VAL LYS GLN SEQRES 3 B 443 TRP PRO LEU THR GLU GLU LYS ILE LYS ALA LEU VAL GLU SEQRES 4 B 443 ILE CYS THR GLU MET GLU LYS GLU GLY LYS ILE SER LYS SEQRES 5 B 443 ILE GLY PRO GLU ASN PRO TYR ASN THR PRO VAL PHE ALA SEQRES 6 B 443 ILE LYS LYS LYS ASP SER THR LYS TRP ARG LYS LEU VAL SEQRES 7 B 443 ASP PHE ARG GLU LEU ASN LYS ARG THR GLN ASP PHE TRP SEQRES 8 B 443 GLU VAL GLN LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS SEQRES 9 B 443 LYS ASN LYS SER VAL THR VAL LEU ASP VAL GLY ASP ALA SEQRES 10 B 443 TYR PHE SER VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR SEQRES 11 B 443 THR ALA PHE THR ILE PRO SER ILE ASN ASN GLU THR PRO SEQRES 12 B 443 GLY ILE ARG TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP SEQRES 13 B 443 LYS GLY SER PRO ALA ILE PHE GLN SER SER MET THR LYS SEQRES 14 B 443 ILE LEU GLU PRO PHE ARG LYS GLN ASN PRO ASP ILE VAL SEQRES 15 B 443 ILE TYR GLN TYR MET ASP ASP LEU TYR VAL GLY SER ASP SEQRES 16 B 443 LEU GLU ILE GLY GLN HIS ARG THR LYS ILE GLU GLU LEU SEQRES 17 B 443 ARG GLN HIS LEU LEU ARG TRP GLY LEU THR THR PRO ASP SEQRES 18 B 443 LYS LYS HIS GLN LYS GLU PRO PRO PHE LEU TRP MET GLY SEQRES 19 B 443 TYR GLU LEU HIS PRO ASP LYS TRP THR VAL GLN PRO ILE SEQRES 20 B 443 VAL LEU PRO GLU LYS ASP SER TRP THR VAL ASN ASP ILE SEQRES 21 B 443 GLN LYS LEU VAL GLY LYS LEU ASN TRP ALA SER GLN ILE SEQRES 22 B 443 TYR PRO GLY ILE LYS VAL ARG GLN LEU CYS LYS LEU LEU SEQRES 23 B 443 ARG GLY THR LYS ALA LEU THR GLU VAL ILE PRO LEU THR SEQRES 24 B 443 GLU GLU ALA GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE SEQRES 25 B 443 LEU LYS GLU PRO VAL HIS GLY VAL TYR TYR ASP PRO SER SEQRES 26 B 443 LYS ASP LEU ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY SEQRES 27 B 443 GLN TRP THR TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN SEQRES 28 B 443 LEU LYS THR GLY LYS TYR ALA ARG MET ARG GLY ALA HIS SEQRES 29 B 443 THR ASN ASP VAL LYS GLN LEU THR GLU ALA VAL GLN LYS SEQRES 30 B 443 ILE THR THR GLU SER ILE VAL ILE TRP GLY LYS THR PRO SEQRES 31 B 443 LYS PHE LYS LEU PRO ILE GLN LYS GLU THR TRP GLU THR SEQRES 32 B 443 TRP TRP THR GLU TYR TRP GLN ALA THR TRP ILE PRO GLU SEQRES 33 B 443 TRP GLU PHE VAL ASN THR PRO PRO LEU VAL LYS LEU TRP SEQRES 34 B 443 TYR GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA GLU THR SEQRES 35 B 443 PHE HET LP8 A 601 18 HET MN A 602 1 HET MN A 603 1 HET NVP A 701 20 HETNAM LP8 3-CYCLOPENTYL-1,4-DIHYDROXY-1,8-NAPHTHYRIDIN-2(1H)-ONE HETNAM MN MANGANESE (II) ION 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 HETSYN NVP NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE FORMUL 3 LP8 C13 H14 N2 O3 FORMUL 4 MN 2(MN 2+) FORMUL 6 NVP C15 H14 N4 O FORMUL 7 HOH *175(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 PHE A 124 ALA A 129 5 6 HELIX 6 6 GLY A 155 GLN A 174 1 20 HELIX 7 7 GLU A 194 TRP A 212 1 19 HELIX 8 8 THR A 253 SER A 268 1 16 HELIX 9 9 VAL A 276 LEU A 282 1 7 HELIX 10 10 THR A 296 LYS A 311 1 16 HELIX 11 11 ASN A 363 GLY A 384 1 22 HELIX 12 12 GLN A 394 TYR A 405 1 12 HELIX 13 13 THR A 473 ASP A 488 1 16 HELIX 14 14 SER A 499 ALA A 508 1 10 HELIX 15 15 SER A 515 LYS A 528 1 14 HELIX 16 16 ILE A 542 ALA A 554 1 13 HELIX 17 17 THR B 27 GLU B 44 1 18 HELIX 18 18 PHE B 77 ARG B 83 1 7 HELIX 19 19 THR B 84 GLU B 89 1 6 HELIX 20 20 GLY B 112 VAL B 118 5 7 HELIX 21 21 PHE B 124 ALA B 129 5 6 HELIX 22 22 SER B 134 GLU B 138 5 5 HELIX 23 23 LYS B 154 ASN B 175 1 22 HELIX 24 24 GLU B 194 ARG B 211 1 18 HELIX 25 25 HIS B 235 TRP B 239 5 5 HELIX 26 26 VAL B 254 TYR B 271 1 18 HELIX 27 27 VAL B 276 LYS B 281 1 6 HELIX 28 28 ALA B 299 GLU B 312 1 14 HELIX 29 29 ASN B 363 GLY B 384 1 22 HELIX 30 30 GLN B 394 TRP B 406 1 13 HELIX 31 31 LEU B 422 TYR B 427 1 6 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 ILE A 132 O ILE A 142 SHEET 1 B 2 VAL A 60 ILE A 63 0 SHEET 2 B 2 ARG A 72 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 VAL A 179 O GLY A 190 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 LEU A 349 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 LEU A 469 0 SHEET 2 G 5 GLY A 453 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 TYR A 532 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 ILE B 132 O ILE B 142 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 THR B 107 O VAL B 189 SHEET 4 J 4 TYR B 232 LEU B 234 -1 O LEU B 234 N VAL B 106 SHEET 1 K 2 TRP B 252 THR B 253 0 SHEET 2 K 2 VAL B 292 ILE B 293 -1 O ILE B 293 N TRP B 252 SHEET 1 L 5 ASN B 348 ALA B 355 0 SHEET 2 L 5 GLN B 336 TYR B 342 -1 N ILE B 341 O LYS B 350 SHEET 3 L 5 ILE B 326 GLY B 333 -1 N ILE B 326 O TYR B 342 SHEET 4 L 5 LYS B 388 LEU B 391 1 O LYS B 390 N ALA B 327 SHEET 5 L 5 TRP B 414 PHE B 416 1 O GLU B 415 N PHE B 389 LINK OD1 ASP A 443 MN MN A 602 1555 1555 2.00 LINK OD2 ASP A 443 MN MN A 603 1555 1555 2.00 LINK OE2 GLU A 478 MN MN A 603 1555 1555 2.08 LINK OD1 ASP A 498 MN MN A 603 1555 1555 2.09 LINK OD1 ASP A 549 MN MN A 602 1555 1555 2.23 LINK O LP8 A 601 MN MN A 602 1555 1555 2.25 LINK O3 LP8 A 601 MN MN A 602 1555 1555 2.41 LINK O LP8 A 601 MN MN A 603 1555 1555 2.04 LINK N9 LP8 A 601 MN MN A 603 1555 1555 2.39 CISPEP 1 PRO A 225 PRO A 226 0 2.26 CISPEP 2 PRO A 420 PRO A 421 0 0.00 SITE 1 AC1 8 ASP A 443 GLU A 478 ASP A 498 HIS A 539 SITE 2 AC1 8 ASP A 549 HOH A 594 MN A 602 MN A 603 SITE 1 AC2 4 ASP A 443 ASP A 549 LP8 A 601 MN A 603 SITE 1 AC3 5 ASP A 443 GLU A 478 ASP A 498 LP8 A 601 SITE 2 AC3 5 MN A 602 SITE 1 AC4 12 LEU A 100 LYS A 101 VAL A 179 TYR A 181 SITE 2 AC4 12 TYR A 188 GLY A 190 PHE A 227 TRP A 229 SITE 3 AC4 12 LEU A 234 HIS A 235 TYR A 318 HOH A 649 CRYST1 118.784 155.264 155.244 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 0.008419 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006441 0.00000