HEADER TRANSFERASE 03-JUN-10 3NBP TITLE HIV-1 REVERSE TRANSCRIPTASE WITH AMINOPYRIMIDINE INHIBITOR 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: REVERSE TRANSCRIPTASE/RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIV-1 RT P66; COMPND 5 EC: 2.7.7.49, 2.7.7.7, 3.1.26.13; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: P51 RT; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: HIV-1 RT P51; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SOURCE 3 SUBTYPE B; SOURCE 4 ORGANISM_COMMON: HIV-1; SOURCE 5 ORGANISM_TAXID: 11706; SOURCE 6 STRAIN: ISOLATE HXB2; 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; SOURCE 13 ORGANISM_COMMON: HIV-1; SOURCE 14 ORGANISM_TAXID: 11706; SOURCE 15 STRAIN: ISOLATE HXB2; SOURCE 16 GENE: GAG-POL; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIV, RT, REVERSE TRANSCRIPTASE, TRANSFERASE RNA-DIRECTED DNA KEYWDS 2 POLYMERASE, NUCLEOTIDYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.F.HARRIS,A.G.VILLASENOR REVDAT 2 21-FEB-24 3NBP 1 REMARK LINK REVDAT 1 18-AUG-10 3NBP 0 JRNL AUTH D.J.KERTESZ,C.BROTHERTON-PLEISS,M.YANG,Z.WANG,X.LIN,Z.QIU, JRNL AUTH 2 D.R.HIRSCHFELD,S.GLEASON,T.MIRZADEGAN,P.W.DUNTEN,S.F.HARRIS, JRNL AUTH 3 A.G.VILLASENOR,J.Q.HANG,G.M.HEILEK,K.KLUMPP JRNL TITL DISCOVERY OF PIPERIDIN-4-YL-AMINOPYRIMIDINES AS HIV-1 JRNL TITL 2 REVERSE TRANSCRIPTASE INHIBITORS. N-BENZYL DERIVATIVES WITH JRNL TITL 3 BROAD POTENCY AGAINST RESISTANT MUTANT VIRUSES. JRNL REF BIOORG.MED.CHEM.LETT. V. 20 4215 2010 JRNL REFN ISSN 0960-894X JRNL PMID 20538456 JRNL DOI 10.1016/J.BMCL.2010.05.040 REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.9.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 28590 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1463 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 14 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.95 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.06 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2191 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2528 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2069 REMARK 3 BIN R VALUE (WORKING SET) : 0.2498 REMARK 3 BIN FREE R VALUE : 0.3053 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.57 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 122 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7812 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 77.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 21.13720 REMARK 3 B22 (A**2) : 12.84040 REMARK 3 B33 (A**2) : -33.97760 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.405 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.911 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.882 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 8059 ; 2.000 ; NULL REMARK 3 BOND ANGLES : 10956 ; 2.000 ; NULL REMARK 3 TORSION ANGLES : 2789 ; 2.000 ; NULL REMARK 3 TRIGONAL CARBON PLANES : 226 ; 2.000 ; NULL REMARK 3 GENERAL PLANES : 1093 ; 5.000 ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS : 8059 ; 20.000 ; NULL REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 1043 ; 5.000 ; NULL REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 9179 ; 4.000 ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.18 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.52 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 22.27 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NBP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 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 : 28615 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 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 (%) : 95.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11500 REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.71200 REMARK 200 FOR SHELL : 1.480 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 (%): 59.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M NA-MALONATE, 50MM KPO4 PH 7.2, REMARK 280 5% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 77.23200 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 77.23200 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 59.34300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 76.43450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 59.34300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 76.43450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 77.23200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.34300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 76.43450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 77.23200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 59.34300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 76.43450 REMARK 290 SMTRY3 8 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: 5590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 LYS A 65 REMARK 465 LYS A 66 REMARK 465 ASP A 67 REMARK 465 LYS A 558 REMARK 465 VAL A 559 REMARK 465 LEU A 560 REMARK 465 PHE A 561 REMARK 465 PRO B 1 REMARK 465 ILE B 2 REMARK 465 SER B 3 REMARK 465 PRO B 4 REMARK 465 LYS B 65 REMARK 465 LYS B 66 REMARK 465 ASP B 67 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 LEU B 283 REMARK 465 ARG B 284 REMARK 465 GLY B 285 REMARK 465 ARG B 356 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 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 ILE A 556 CG1 CG2 CD1 REMARK 470 ARG A 557 CG 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 ILE A 5 134.68 -38.38 REMARK 500 ALA A 114 -72.73 -27.82 REMARK 500 ASN A 137 19.76 58.41 REMARK 500 MET A 184 -126.41 57.53 REMARK 500 ASP A 185 44.57 -101.01 REMARK 500 ILE A 195 -18.62 -39.17 REMARK 500 PRO A 217 -97.79 -79.16 REMARK 500 GLN A 222 142.01 -39.22 REMARK 500 MET A 230 22.07 49.54 REMARK 500 PRO A 243 109.49 -23.75 REMARK 500 THR A 286 -93.97 -72.32 REMARK 500 LYS A 287 126.43 59.44 REMARK 500 PRO A 345 114.31 -30.32 REMARK 500 PRO A 412 -163.11 -61.39 REMARK 500 LYS A 451 7.85 59.14 REMARK 500 LYS A 454 60.58 -156.23 REMARK 500 ALA A 508 -9.20 -51.37 REMARK 500 HIS A 539 6.57 53.83 REMARK 500 ALA A 554 92.35 -59.37 REMARK 500 ILE A 556 88.97 61.72 REMARK 500 LYS B 13 148.82 162.13 REMARK 500 ILE B 63 -166.92 -125.81 REMARK 500 GLN B 85 -54.31 -2.14 REMARK 500 VAL B 90 -63.15 -98.67 REMARK 500 LEU B 92 28.02 -147.75 REMARK 500 MET B 184 -115.03 53.31 REMARK 500 TRP B 212 -52.38 86.69 REMARK 500 LEU B 214 89.68 -152.33 REMARK 500 LYS B 281 24.81 -76.41 REMARK 500 PRO B 345 125.40 -29.79 REMARK 500 PHE B 346 -10.75 66.21 REMARK 500 TYR B 427 33.46 -99.32 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 GLU A 478 OE2 71.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN 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 JGZ A 562 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M8P RELATED DB: PDB REMARK 900 HIV RT WITH TMC-125 AMINOPYRIMIDINE INHIBITOR REMARK 900 RELATED ID: 3M8Q RELATED DB: PDB REMARK 900 HIV RT WITH AMINOPYRIMIDINE 1 INHIBITOR DBREF 3NBP A 1 561 UNP P04585 POL_HV1H2 588 1148 DBREF 3NBP B 1 440 UNP P04585 POL_HV1H2 588 1027 SEQRES 1 A 561 PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS LEU LYS SEQRES 2 A 561 PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP PRO LEU SEQRES 3 A 561 THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE CYS THR SEQRES 4 A 561 GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE GLY PRO SEQRES 5 A 561 GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE LYS LYS SEQRES 6 A 561 LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP PHE ARG SEQRES 7 A 561 GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU VAL GLN SEQRES 8 A 561 LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS LYS LYS SEQRES 9 A 561 SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR PHE SER SEQRES 10 A 561 VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR ALA PHE SEQRES 11 A 561 THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY ILE ARG SEQRES 12 A 561 TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS GLY SER SEQRES 13 A 561 PRO ALA ILE PHE GLN SER SER MET THR LYS ILE LEU GLU SEQRES 14 A 561 PRO PHE ARG LYS GLN ASN PRO ASP ILE VAL ILE TYR GLN SEQRES 15 A 561 TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU GLU ILE SEQRES 16 A 561 GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG GLN HIS SEQRES 17 A 561 LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS LYS HIS SEQRES 18 A 561 GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR GLU LEU SEQRES 19 A 561 HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL LEU PRO SEQRES 20 A 561 GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN LYS LEU SEQRES 21 A 561 VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR PRO GLY SEQRES 22 A 561 ILE LYS VAL ARG GLN LEU CYS LYS LEU LEU ARG GLY THR SEQRES 23 A 561 LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU GLU ALA SEQRES 24 A 561 GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU LYS GLU SEQRES 25 A 561 PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS ASP LEU SEQRES 26 A 561 ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN TRP THR SEQRES 27 A 561 TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU LYS THR SEQRES 28 A 561 GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR ASN ASP SEQRES 29 A 561 VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE THR THR SEQRES 30 A 561 GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS PHE LYS SEQRES 31 A 561 LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP TRP THR SEQRES 32 A 561 GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP GLU PHE SEQRES 33 A 561 VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR GLN LEU SEQRES 34 A 561 GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE TYR VAL SEQRES 35 A 561 ASP GLY ALA ALA ASN ARG GLU THR LYS LEU GLY LYS ALA SEQRES 36 A 561 GLY TYR VAL THR ASN ARG GLY ARG GLN LYS VAL VAL THR SEQRES 37 A 561 LEU THR ASP THR THR ASN GLN LYS THR GLU LEU GLN ALA SEQRES 38 A 561 ILE TYR LEU ALA LEU GLN ASP SER GLY LEU GLU VAL ASN SEQRES 39 A 561 ILE VAL THR ASP SER GLN TYR ALA LEU GLY ILE ILE GLN SEQRES 40 A 561 ALA GLN PRO ASP GLN SER GLU SER GLU LEU VAL ASN GLN SEQRES 41 A 561 ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS VAL TYR LEU SEQRES 42 A 561 ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY GLY ASN GLU SEQRES 43 A 561 GLN VAL ASP LYS LEU VAL SER ALA GLY ILE ARG LYS VAL SEQRES 44 A 561 LEU PHE 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 MN A 601 1 HET MN A 602 1 HET JGZ A 562 34 HETNAM MN MANGANESE (II) ION HETNAM JGZ 4-(4-{[4-(4-CYANO-2,6-DIMETHYLPHENOXY)PYRIMIDIN-2- HETNAM 2 JGZ YL]AMINO}PIPERIDIN-1-YL)BENZENESULFONAMIDE FORMUL 3 MN 2(MN 2+) FORMUL 5 JGZ C24 H26 N6 O3 S FORMUL 6 HOH *91(H2 O) HELIX 1 1 THR A 27 LYS A 43 1 17 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 LYS A 126 1 6 HELIX 6 6 TYR A 127 ALA A 129 5 3 HELIX 7 7 SER A 134 GLU A 138 5 5 HELIX 8 8 GLY A 155 ASN A 175 1 21 HELIX 9 9 GLU A 194 TRP A 212 1 19 HELIX 10 10 THR A 253 SER A 268 1 16 HELIX 11 11 VAL A 276 ARG A 284 1 9 HELIX 12 12 THR A 296 LEU A 310 1 15 HELIX 13 13 ASN A 363 TRP A 383 1 21 HELIX 14 14 GLN A 394 TYR A 405 1 12 HELIX 15 15 THR A 473 SER A 489 1 17 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 GLY A 544 ALA A 554 1 11 HELIX 19 19 THR B 27 GLU B 44 1 18 HELIX 20 20 PHE B 77 GLN B 85 1 9 HELIX 21 21 GLN B 85 VAL B 90 1 6 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 LYS B 281 1 6 HELIX 31 31 THR B 296 GLU B 312 1 17 HELIX 32 32 ASN B 363 GLY B 384 1 22 HELIX 33 33 GLN B 394 TRP B 402 1 9 HELIX 34 34 THR B 403 TYR B 405 5 3 HELIX 35 35 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 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 ARG A 72 N ILE A 63 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 4 PHE A 227 TRP A 229 0 SHEET 2 D 4 TYR A 232 LEU A 234 -1 O LEU A 234 N PHE A 227 SHEET 3 D 4 LYS A 238 VAL A 241 -1 O THR A 240 N GLU A 233 SHEET 4 D 4 GLY A 316 VAL A 317 -1 O GLY A 316 N TRP A 239 SHEET 1 E 5 ASN A 348 ALA A 355 0 SHEET 2 E 5 GLN A 336 TYR A 342 -1 N TYR A 339 O GLY A 352 SHEET 3 E 5 ILE A 326 LYS A 331 -1 N GLN A 330 O THR A 338 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 VAL A 466 0 SHEET 2 G 5 GLY A 453 THR A 459 -1 N TYR A 457 O LYS A 465 SHEET 3 G 5 THR A 439 ALA A 446 -1 N TYR A 441 O VAL A 458 SHEET 4 G 5 GLU A 492 THR A 497 1 O VAL A 496 N VAL A 442 SHEET 5 G 5 LYS A 530 TRP A 535 1 O TYR A 532 N VAL A 493 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 ARG B 72 N ILE B 63 SHEET 1 J 3 SER B 105 ASP B 110 0 SHEET 2 J 3 ASP B 186 SER B 191 -1 O VAL B 189 N THR B 107 SHEET 3 J 3 VAL B 179 TYR B 183 -1 N TYR B 181 O TYR B 188 SHEET 1 K 5 ASN B 348 TYR B 354 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 388 N ALA B 327 SHEET 5 K 5 TRP B 414 PHE B 416 1 O GLU B 415 N LEU B 391 LINK OD1 ASP A 443 MN MN A 602 1555 1555 2.76 LINK OE1 GLU A 478 MN MN A 601 1555 1555 2.02 LINK OE2 GLU A 478 MN MN A 602 1555 1555 2.30 CISPEP 1 PRO A 225 PRO A 226 0 0.44 CISPEP 2 PRO A 420 PRO A 421 0 2.47 SITE 1 AC1 5 VAL A 442 ASP A 443 GLU A 478 THR A 497 SITE 2 AC1 5 ASP A 498 SITE 1 AC2 3 ASP A 443 GLU A 478 ASP A 498 SITE 1 AC3 14 LEU A 100 LYS A 101 LYS A 103 VAL A 106 SITE 2 AC3 14 VAL A 179 TYR A 181 TYR A 188 PRO A 225 SITE 3 AC3 14 PHE A 227 TRP A 229 LEU A 234 HIS A 235 SITE 4 AC3 14 PRO A 236 TYR A 318 CRYST1 118.686 152.869 154.464 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 0.008426 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006542 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006474 0.00000