HEADER TRANSFERASE 12-JUL-99 1QE1 TITLE CRYSTAL STRUCTURE OF 3TC-RESISTANT M184I MUTANT OF HIV-1 REVERSE TITLE 2 TRANSCRIPTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: REVERSE TRANSCRIPTASE, SUBUNIT P66; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SUBUNIT A (P66), RESIDUES 168-725; COMPND 5 SYNONYM: RT; COMPND 6 EC: 2.7.7.49; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: REVERSE TRANSCRIPTASE, SUBUNIT P51; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: SUBUNIT B (P51), RESIDUES 168-594; COMPND 13 SYNONYM: RT; COMPND 14 EC: 2.7.7.49; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 BH10; SOURCE 3 ORGANISM_TAXID: 11678; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 BH10; SOURCE 8 ORGANISM_TAXID: 11678; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIV, REVERSE TRANSCRIPTASE, 3TC, RESISTANCE, MUTANT, DNA POLYMERASE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.G.SARAFIANOS,K.DAS,J.DING,S.H.HUGHES,E.ARNOLD REVDAT 6 14-FEB-24 1QE1 1 REMARK REVDAT 5 03-NOV-21 1QE1 1 SEQADV REVDAT 4 24-FEB-09 1QE1 1 VERSN REVDAT 3 01-APR-03 1QE1 1 JRNL REVDAT 2 20-MAR-00 1QE1 1 SEQRES SEQADV REVDAT 1 30-AUG-99 1QE1 0 JRNL AUTH S.G.SARAFIANOS,K.DAS,A.D.CLARK JR.,J.DING,P.L.BOYER, JRNL AUTH 2 S.H.HUGHES,E.ARNOLD JRNL TITL LAMIVUDINE (3TC) RESISTANCE IN HIV-1 REVERSE TRANSCRIPTASE JRNL TITL 2 INVOLVES STERIC HINDRANCE WITH BETA-BRANCHED AMINO ACIDS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 10027 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 10468556 JRNL DOI 10.1073/PNAS.96.18.10027 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.HSIOU,J.DING,K.DAS,A.D.CLARK JR.,S.H.HUGHES,E.ARNOLD REMARK 1 TITL STRUCTURE OF UNLIGANDED HIV-1 REVERSE TRANSCRIPTASE AT 2.7 A REMARK 1 TITL 2 RESOLUTION: IMPLICATIONS OF CONFORMATIONAL CHANGES FOR REMARK 1 TITL 3 POLYMERIZATION AND INHIBITION MECHANISMS REMARK 1 REF STRUCTURE V. 4 853 1996 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(96)00091-3 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.DING,K.DAS,Y.HSIOU,S.G.SARAFIANOS,A.D.CLARK JR., REMARK 1 AUTH 2 A.JACOBO-MOLINA,C.TANTILLO,S.H.HUGHES,E.ARNOLD REMARK 1 TITL STRUCTURE AND FUNCTIONAL IMPLICATIONS OF THE POLYMERASE REMARK 1 TITL 2 ACTIVE SITE REGION IN A COMPLEX OF HIV-1 RT WITH A REMARK 1 TITL 3 DOUBLE-STRANDED DNA AND AN ANTIBODY FAB FRAGMENT AT 2.8 REMARK 1 TITL 4 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 284 1095 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1998.2208 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 31250 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 SET) : 0.259 REMARK 3 FREE R VALUE : 0.346 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1426 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 7699 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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) : 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QE1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000009329. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 108 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.928 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35177 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 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: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, GLYCEROL, BIS-TRIS, AMMONIUM REMARK 280 SULFATE, PH 6.8, VAPOR DIFFUSION, HANGING 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 119.30000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 119.30000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.35000 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 300 REMARK: HETERODIMER, OF TWO SUBUNITS, P66 AND P51. P51 CONTAINS THE REMARK 300 N-TERMINAL 440 RESIDUES OF THE P66 SUBUNIT. 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: 5300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 ARG A 557 REMARK 465 LYS A 558 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 22 CG CD CE NZ REMARK 470 GLU A 28 CG CD OE1 OE2 REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 TRP A 71 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 71 CZ3 CH2 REMARK 470 SER A 134 OG REMARK 470 ILE A 135 CG1 CG2 CD1 REMARK 470 ASN A 136 CG OD1 ND2 REMARK 470 THR A 139 OG1 CG2 REMARK 470 GLU A 169 CG CD OE1 OE2 REMARK 470 ASP A 177 CG OD1 OD2 REMARK 470 ILE A 184 CG1 CG2 CD1 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 LYS A 219 CG CD CE NZ REMARK 470 GLN A 242 CG CD OE1 NE2 REMARK 470 GLN A 278 CG CD OE1 NE2 REMARK 470 GLU A 291 CG CD OE1 OE2 REMARK 470 GLU A 297 CG CD OE1 OE2 REMARK 470 GLU A 305 CG CD OE1 OE2 REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 GLU A 312 CG CD OE1 OE2 REMARK 470 GLN A 336 CG CD OE1 NE2 REMARK 470 ARG A 356 CG CD NE CZ NH1 NH2 REMARK 470 MET A 357 CG SD CE REMARK 470 ARG A 358 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 404 CG CD OE1 OE2 REMARK 470 GLU A 413 CG CD OE1 OE2 REMARK 470 LYS A 424 CG CD CE NZ REMARK 470 ARG A 448 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 451 CG CD CE NZ REMARK 470 LYS A 512 CG CD CE NZ REMARK 470 GLU A 514 CG CD OE1 OE2 REMARK 470 ASP A 549 CG OD1 OD2 REMARK 470 LYS A 550 CG CD CE NZ REMARK 470 ILE A 556 CG1 CG2 CD1 REMARK 470 GLU B 36 CG CD OE1 OE2 REMARK 470 ASP B 67 CG OD1 OD2 REMARK 470 THR B 69 OG1 CG2 REMARK 470 TRP B 88 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 88 CZ3 CH2 REMARK 470 GLU B 89 CG CD OE1 OE2 REMARK 470 LYS B 173 CG CD CE NZ REMARK 470 GLN B 197 CG CD OE1 NE2 REMARK 470 ASP B 218 CG OD1 OD2 REMARK 470 LYS B 238 CG CD CE NZ REMARK 470 LYS B 281 CG CD CE NZ REMARK 470 LEU B 295 CG CD1 CD2 REMARK 470 GLU B 297 CG CD OE1 OE2 REMARK 470 GLU B 305 CG CD OE1 OE2 REMARK 470 ASN B 306 CG OD1 ND2 REMARK 470 GLU B 308 CG CD OE1 OE2 REMARK 470 ARG B 356 CG CD NE CZ NH1 NH2 REMARK 470 MET B 357 CG SD CE REMARK 470 ARG B 358 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 361 CG ND1 CD2 CE1 NE2 REMARK 470 THR B 362 OG1 CG2 REMARK 470 GLN B 407 CG CD OE1 NE2 REMARK 470 LYS B 424 CG CD CE NZ REMARK 470 LEU B 425 CG CD1 CD2 REMARK 470 TYR B 427 CG CD1 CD2 CE1 CE2 CZ OH REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 225 C - N - CA ANGL. DEV. = 13.3 DEGREES REMARK 500 PRO B 55 C - N - CA ANGL. DEV. = 10.9 DEGREES REMARK 500 PRO B 97 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 PRO B 140 C - N - CA ANGL. DEV. = 10.7 DEGREES REMARK 500 PRO B 392 C - N - CA ANGL. DEV. = 9.8 DEGREES 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 PRO A 4 40.40 -93.81 REMARK 500 LEU A 26 -146.98 -95.22 REMARK 500 ILE A 50 -166.65 -117.20 REMARK 500 PRO A 52 11.51 -62.93 REMARK 500 ARG A 78 -38.63 -36.82 REMARK 500 ASN A 81 -9.62 -57.18 REMARK 500 GLN A 85 157.09 -33.09 REMARK 500 LEU A 100 155.20 -47.45 REMARK 500 LYS A 104 -72.53 -11.15 REMARK 500 SER A 117 -70.80 -81.44 REMARK 500 PHE A 124 3.28 -56.46 REMARK 500 ASN A 137 11.88 -68.65 REMARK 500 TYR A 144 -166.25 -120.80 REMARK 500 SER A 156 -63.72 -19.98 REMARK 500 PRO A 176 7.26 -46.51 REMARK 500 ILE A 184 -124.96 47.76 REMARK 500 ASP A 185 53.13 -113.78 REMARK 500 ILE A 195 -56.71 -4.84 REMARK 500 LYS A 223 87.26 -15.40 REMARK 500 PRO A 225 -52.68 -15.22 REMARK 500 VAL A 276 -13.47 -141.54 REMARK 500 ALA A 288 104.31 53.66 REMARK 500 LEU A 310 6.73 -57.95 REMARK 500 GLN A 332 -116.70 -148.52 REMARK 500 GLN A 334 27.47 26.36 REMARK 500 GLN A 343 -52.23 -121.36 REMARK 500 PHE A 346 -10.31 76.56 REMARK 500 LYS A 366 4.31 -62.03 REMARK 500 THR A 369 -76.09 -39.13 REMARK 500 ILE A 393 122.18 -176.18 REMARK 500 PRO A 412 -172.27 -65.73 REMARK 500 PRO A 420 -100.21 -22.74 REMARK 500 PRO A 421 66.84 -51.72 REMARK 500 PHE A 440 96.29 -67.62 REMARK 500 ASP A 443 -176.37 -173.88 REMARK 500 ALA A 445 -161.83 -179.67 REMARK 500 ALA A 446 -162.04 -176.96 REMARK 500 ALA A 455 105.83 -176.19 REMARK 500 VAL A 458 63.33 -167.85 REMARK 500 THR A 459 173.40 -48.48 REMARK 500 LYS A 461 3.25 -68.71 REMARK 500 ARG A 463 166.45 -44.25 REMARK 500 LYS A 465 172.34 169.25 REMARK 500 ASN A 474 -16.98 -49.77 REMARK 500 LEU A 484 -71.58 -54.40 REMARK 500 ALA A 485 -26.30 -38.28 REMARK 500 LEU A 491 0.62 -62.66 REMARK 500 ILE A 495 158.31 -46.35 REMARK 500 LYS A 528 -171.42 -46.85 REMARK 500 GLU A 529 -37.33 -131.62 REMARK 500 REMARK 500 THIS ENTRY HAS 103 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 144 0.09 SIDE CHAIN REMARK 500 TYR A 232 0.07 SIDE CHAIN REMARK 500 PHE B 160 0.08 SIDE CHAIN REMARK 500 TYR B 183 0.07 SIDE CHAIN REMARK 500 TYR B 342 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C9R RELATED DB: PDB REMARK 900 CONTAINS THE SAME PROTEIN IN COMPLEX WITH A DOUBLE STRANDED DNA REMARK 900 FRAGMENT AND A FAB MONOCLONAL ANTIBODY FRAGMENT REMARK 900 RELATED ID: 1DLO RELATED DB: PDB REMARK 900 STRUCTURE OF WILD-TYPE UNLIGANDED HIV-1 REVERSE TRANSCRIPTASE REMARK 900 RELATED ID: 2HMI RELATED DB: PDB REMARK 900 STRUCTURE OF WILD-TYPE HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH REMARK 900 DNA AND A FAB MONOCLONAL ANTIBODY FRAGMENT DBREF 1QE1 A 1 558 UNP P03366 POL_HV1B1 168 725 DBREF 1QE1 B 1 427 UNP P03366 POL_HV1B1 168 594 SEQADV 1QE1 ILE A 184 UNP P03366 MET 351 ENGINEERED MUTATION SEQADV 1QE1 SER A 280 UNP P03366 CYS 447 ENGINEERED MUTATION SEQADV 1QE1 ILE B 184 UNP P03366 MET 351 ENGINEERED MUTATION SEQADV 1QE1 SER B 280 UNP P03366 CYS 447 ENGINEERED MUTATION SEQRES 1 A 558 PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS LEU LYS SEQRES 2 A 558 PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP PRO LEU SEQRES 3 A 558 THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE CYS THR SEQRES 4 A 558 GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE GLY PRO SEQRES 5 A 558 GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE LYS LYS SEQRES 6 A 558 LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP PHE ARG SEQRES 7 A 558 GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU VAL GLN SEQRES 8 A 558 LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS LYS LYS SEQRES 9 A 558 SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR PHE SER SEQRES 10 A 558 VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR ALA PHE SEQRES 11 A 558 THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY ILE ARG SEQRES 12 A 558 TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS GLY SER SEQRES 13 A 558 PRO ALA ILE PHE GLN SER SER MET THR LYS ILE LEU GLU SEQRES 14 A 558 PRO PHE LYS LYS GLN ASN PRO ASP ILE VAL ILE TYR GLN SEQRES 15 A 558 TYR ILE ASP ASP LEU TYR VAL GLY SER ASP LEU GLU ILE SEQRES 16 A 558 GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG GLN HIS SEQRES 17 A 558 LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS LYS HIS SEQRES 18 A 558 GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR GLU LEU SEQRES 19 A 558 HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL LEU PRO SEQRES 20 A 558 GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN LYS LEU SEQRES 21 A 558 VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR PRO GLY SEQRES 22 A 558 ILE LYS VAL ARG GLN LEU SER LYS LEU LEU ARG GLY THR SEQRES 23 A 558 LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU GLU ALA SEQRES 24 A 558 GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU LYS GLU SEQRES 25 A 558 PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS ASP LEU SEQRES 26 A 558 ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN TRP THR SEQRES 27 A 558 TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU LYS THR SEQRES 28 A 558 GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR ASN ASP SEQRES 29 A 558 VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE THR THR SEQRES 30 A 558 GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS PHE LYS SEQRES 31 A 558 LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP TRP THR SEQRES 32 A 558 GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP GLU PHE SEQRES 33 A 558 VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR GLN LEU SEQRES 34 A 558 GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE TYR VAL SEQRES 35 A 558 ASP GLY ALA ALA ASN ARG GLU THR LYS LEU GLY LYS ALA SEQRES 36 A 558 GLY TYR VAL THR ASN LYS GLY ARG GLN LYS VAL VAL PRO SEQRES 37 A 558 LEU THR ASN THR THR ASN GLN LYS THR GLU LEU GLN ALA SEQRES 38 A 558 ILE TYR LEU ALA LEU GLN ASP SER GLY LEU GLU VAL ASN SEQRES 39 A 558 ILE VAL THR ASP SER GLN TYR ALA LEU GLY ILE ILE GLN SEQRES 40 A 558 ALA GLN PRO ASP LYS SER GLU SER GLU LEU VAL ASN GLN SEQRES 41 A 558 ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS VAL TYR LEU SEQRES 42 A 558 ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY GLY ASN GLU SEQRES 43 A 558 GLN VAL ASP LYS LEU VAL SER ALA GLY ILE ARG LYS SEQRES 1 B 427 PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS LEU LYS SEQRES 2 B 427 PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP PRO LEU SEQRES 3 B 427 THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE CYS THR SEQRES 4 B 427 GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE GLY PRO SEQRES 5 B 427 GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE LYS LYS SEQRES 6 B 427 LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP PHE ARG SEQRES 7 B 427 GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU VAL GLN SEQRES 8 B 427 LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS LYS LYS SEQRES 9 B 427 SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR PHE SER SEQRES 10 B 427 VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR ALA PHE SEQRES 11 B 427 THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY ILE ARG SEQRES 12 B 427 TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS GLY SER SEQRES 13 B 427 PRO ALA ILE PHE GLN SER SER MET THR LYS ILE LEU GLU SEQRES 14 B 427 PRO PHE LYS LYS GLN ASN PRO ASP ILE VAL ILE TYR GLN SEQRES 15 B 427 TYR ILE ASP ASP LEU TYR VAL GLY SER ASP LEU GLU ILE SEQRES 16 B 427 GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG GLN HIS SEQRES 17 B 427 LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS LYS HIS SEQRES 18 B 427 GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR GLU LEU SEQRES 19 B 427 HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL LEU PRO SEQRES 20 B 427 GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN LYS LEU SEQRES 21 B 427 VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR PRO GLY SEQRES 22 B 427 ILE LYS VAL ARG GLN LEU SER LYS LEU LEU ARG GLY THR SEQRES 23 B 427 LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU GLU ALA SEQRES 24 B 427 GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU LYS GLU SEQRES 25 B 427 PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS ASP LEU SEQRES 26 B 427 ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN TRP THR SEQRES 27 B 427 TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU LYS THR SEQRES 28 B 427 GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR ASN ASP SEQRES 29 B 427 VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE THR THR SEQRES 30 B 427 GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS PHE LYS SEQRES 31 B 427 LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP TRP THR SEQRES 32 B 427 GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP GLU PHE SEQRES 33 B 427 VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR HELIX 1 1 THR A 27 GLU A 44 1 18 HELIX 2 2 GLU A 79 THR A 84 1 6 HELIX 3 3 HIS A 96 LEU A 100 5 5 HELIX 4 4 ASP A 113 VAL A 118 1 6 HELIX 5 5 ARG A 125 ALA A 129 5 5 HELIX 6 6 GLY A 155 ASN A 175 1 21 HELIX 7 7 GLU A 194 ARG A 211 1 18 HELIX 8 8 VAL A 254 TYR A 271 1 18 HELIX 9 9 VAL A 276 GLY A 285 1 10 HELIX 10 10 THR A 296 LEU A 310 1 15 HELIX 11 11 ASP A 364 TRP A 383 1 20 HELIX 12 12 GLN A 394 THR A 403 1 10 HELIX 13 13 GLN A 475 ASP A 488 1 14 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 GLY A 543 SER A 553 1 11 HELIX 17 17 THR B 27 GLU B 44 1 18 HELIX 18 18 PHE B 77 THR B 84 1 8 HELIX 19 19 GLY B 99 LYS B 103 5 5 HELIX 20 20 GLY B 112 SER B 117 5 6 HELIX 21 21 GLU B 122 ALA B 129 5 8 HELIX 22 22 SER B 134 GLU B 138 5 5 HELIX 23 23 LYS B 154 PHE B 160 1 7 HELIX 24 24 PHE B 160 ASN B 175 1 16 HELIX 25 25 HIS B 198 TRP B 212 1 15 HELIX 26 26 THR B 253 TYR B 271 1 19 HELIX 27 27 VAL B 276 LYS B 281 1 6 HELIX 28 28 GLU B 298 LYS B 311 1 14 HELIX 29 29 ARG B 358 THR B 362 5 5 HELIX 30 30 ASN B 363 TRP B 383 1 21 HELIX 31 31 GLN B 394 THR B 400 1 7 HELIX 32 32 TRP B 401 TYR B 405 5 5 SHEET 1 A 2 VAL A 60 PHE A 61 0 SHEET 2 A 2 LEU A 74 VAL A 75 -1 O LEU A 74 N PHE A 61 SHEET 1 B 3 SER A 105 ASP A 110 0 SHEET 2 B 3 ASP A 186 SER A 191 -1 O LEU A 187 N LEU A 109 SHEET 3 B 3 VAL A 179 TYR A 183 -1 N VAL A 179 O GLY A 190 SHEET 1 C 2 THR A 131 ILE A 132 0 SHEET 2 C 2 ILE A 142 ARG A 143 -1 N ILE A 142 O ILE A 132 SHEET 1 D 4 PHE A 227 LEU A 228 0 SHEET 2 D 4 TYR A 232 LEU A 234 -1 N LEU A 234 O 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 HIS A 315 VAL A 317 -1 O GLY A 316 N TRP A 239 SHEET 1 E 2 TRP A 252 THR A 253 0 SHEET 2 E 2 VAL A 292 ILE A 293 -1 N ILE A 293 O TRP A 252 SHEET 1 F 5 ASN A 348 TYR A 354 0 SHEET 2 F 5 TRP A 337 TYR A 342 -1 O TRP A 337 N TYR A 354 SHEET 3 F 5 ILE A 326 LYS A 331 -1 O ILE A 326 N TYR A 342 SHEET 4 F 5 LYS A 388 LEU A 391 1 O LYS A 388 N ALA A 327 SHEET 5 F 5 TRP A 414 PHE A 416 1 N GLU A 415 O PHE A 389 SHEET 1 G 2 GLY A 453 LYS A 454 0 SHEET 2 G 2 PRO A 468 LEU A 469 -1 O LEU A 469 N GLY A 453 SHEET 1 H 2 VAL A 496 THR A 497 0 SHEET 2 H 2 ALA A 534 TRP A 535 1 O ALA A 534 N THR A 497 SHEET 1 I 3 ILE B 47 LYS B 49 0 SHEET 2 I 3 ILE B 142 TYR B 146 -1 N GLN B 145 O SER B 48 SHEET 3 I 3 PHE B 130 ILE B 132 -1 O PHE B 130 N TYR B 144 SHEET 1 J 2 VAL B 60 ALA B 62 0 SHEET 2 J 2 LYS B 73 VAL B 75 -1 N LEU B 74 O PHE B 61 SHEET 1 K 4 VAL B 179 GLN B 182 0 SHEET 2 K 4 ASP B 186 GLY B 190 -1 N TYR B 188 O TYR B 181 SHEET 3 K 4 VAL B 106 ASP B 110 -1 N THR B 107 O VAL B 189 SHEET 4 K 4 TYR B 232 LEU B 234 -1 O TYR B 232 N VAL B 108 SHEET 1 L 5 ASN B 348 GLY B 352 0 SHEET 2 L 5 TRP B 337 TYR B 342 -1 N TYR B 339 O GLY B 352 SHEET 3 L 5 ILE B 326 LYS B 331 -1 N ILE B 326 O TYR B 342 SHEET 4 L 5 LYS B 388 LEU B 391 1 O LYS B 388 N ALA B 327 SHEET 5 L 5 TRP B 414 PHE B 416 1 O GLU B 415 N LEU B 391 CRYST1 238.600 72.700 95.300 90.00 105.60 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 0.004190 0.000000 0.001170 0.00000 SCALE2 0.000000 0.013760 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010890 0.00000