1RT6 - Header Asymmetric Unit

HEADER NUCLEOTIDYLTRANSFERASE 29-JUL-98 1RT6

TITLE HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH UC38

COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 REVERSE TRANSCRIPTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.49; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HIV-1 REVERSE TRANSCRIPTASE; COMPND 8 CHAIN: B; COMPND 9 EC: 2.7.7.49; COMPND 10 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HIV-1 M:B_HXB2R; SOURCE 3 ORGANISM_TAXID: 11706; SOURCE 4 STRAIN: HXB2 ISOLATE; SOURCE 5 GENE: POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HIV-1 M:B_HXB2R; SOURCE 10 ORGANISM_TAXID: 11706; SOURCE 11 STRAIN: HXB2 ISOLATE; SOURCE 12 GENE: POL; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562

KEYWDS NUCLEOTIDYLTRANSFERASE, HIV-1 REVERSE TRANSCRIPTASE, AIDS, KEYWDS 2 NONNUCLEOSIDE INHIBITION, DRUG DESIGN

EXPDTA X-RAY DIFFRACTION

AUTHOR J.REN,D.K.STAMMERS,D.I.STUART

REVDAT 2 24-FEB-09 1RT6 1 VERSN REVDAT 1 29-JUL-99 1RT6 0

JRNL AUTH J.REN,R.M.ESNOUF,A.L.HOPKINS,J.WARREN,J.BALZARINI, JRNL AUTH 2 D.I.STUART,D.K.STAMMERS JRNL TITL CRYSTAL STRUCTURES OF HIV-1 REVERSE TRANSCRIPTASE JRNL TITL 2 IN COMPLEX WITH CARBOXANILIDE DERIVATIVES. JRNL REF BIOCHEMISTRY V. 37 14394 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9772165 JRNL DOI 10.1021/BI981309M

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.M.ESNOUF,J.REN,E.F.GARMAN,D.O.SOMERS,C.K.ROSS, REMARK 1 AUTH 2 E.Y.JONES,D.K.STAMMERS,D.I.STUART REMARK 1 TITL CONTINUOUS AND DISCONTINUOUS CHANGES IN THE UNIT REMARK 1 TITL 2 CELL OF HIV-1 REVERSE TRANSCRIPTASE CRYSTALS ON REMARK 1 TITL 3 DEHYDRATION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 54 938 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.REN,R.M.ESNOUF,A.L.HOPKINS,E.Y.JONES,I.KIRBY, REMARK 1 AUTH 2 J.KEELING,C.K.ROSS,B.A.LARDER,D.I.STUART, REMARK 1 AUTH 3 D.K.STAMMERS REMARK 1 TITL 3'-AZIDO-3'-DEOXYTHYMIDINE DRUG RESISTANCE REMARK 1 TITL 2 MUTATIONS IN HIV-1 REVERSE TRANSCRIPTASE CAN REMARK 1 TITL 3 INDUCE LONG RANGE CONFORMATIONAL CHANGES REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 95 9518 1998 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.M.ESNOUF,J.REN,A.L.HOPKINS,C.K.ROSS,E.Y.JONES, REMARK 1 AUTH 2 D.K.STAMMERS,D.I.STUART REMARK 1 TITL UNIQUE FEATURES IN THE STRUCTURE OF THE COMPLEX REMARK 1 TITL 2 BETWEEN HIV-1 REVERSE TRANSCRIPTASE AND THE REMARK 1 TITL 3 BIS(HETEROARYL)PIPERAZINE (BHAP) U-90152 EXPLAIN REMARK 1 TITL 4 RESISTANCE MUTATIONS FOR THIS NONNUCLEOSIDE REMARK 1 TITL 5 INHIBITOR REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 94 3984 1997 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.L.HOPKINS,J.REN,R.M.ESNOUF,B.E.WILLCOX,E.Y.JONES, REMARK 1 AUTH 2 C.ROSS,T.MIYASAKA,R.T.WALKER,H.TANAKA,D.K.STAMMERS, REMARK 1 AUTH 3 D.I.STUART REMARK 1 TITL COMPLEXES OF HIV-1 REVERSE TRANSCRIPTASE WITH REMARK 1 TITL 2 INHIBITORS OF THE HEPT SERIES REVEAL REMARK 1 TITL 3 CONFORMATIONAL CHANGES RELEVANT TO THE DESIGN OF REMARK 1 TITL 4 POTENT NON-NUCLEOSIDE INHIBITORS REMARK 1 REF J.MED.CHEM. V. 39 1589 1996 REMARK 1 REFN ISSN 0022-2623 REMARK 1 REFERENCE 5 REMARK 1 AUTH J.REN,R.ESNOUF,A.HOPKINS,C.ROSS,Y.JONES,D.STAMMERS, REMARK 1 AUTH 2 D.STUART REMARK 1 TITL THE STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE REMARK 1 TITL 2 COMPLEXED WITH 9-CHLORO-TIBO: LESSONS FOR REMARK 1 TITL 3 INHIBITOR DESIGN REMARK 1 REF STRUCTURE V. 3 915 1995 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 6 REMARK 1 AUTH J.REN,R.ESNOUF,E.GARMAN,D.SOMERS,C.ROSS,I.KIRBY, REMARK 1 AUTH 2 J.KEELING,G.DARBY,Y.JONES,D.STUART,D.STAMMERS REMARK 1 TITL HIGH RESOLUTION STRUCTURES OF HIV-1 RT FROM FOUR REMARK 1 TITL 2 RT-INHIBITOR COMPLEXES REMARK 1 REF NAT.STRUCT.BIOL. V. 2 293 1995 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 7 REMARK 1 AUTH R.ESNOUF,J.REN,C.ROSS,Y.JONES,D.STAMMERS,D.STUART REMARK 1 TITL MECHANISM OF INHIBITION OF HIV-1 REVERSE REMARK 1 TITL 2 TRANSCRIPTASE BY NON-NUCLEOSIDE INHIBITORS REMARK 1 REF NAT.STRUCT.BIOL. V. 2 303 1995 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 8 REMARK 1 AUTH D.K.STAMMERS,D.O.SOMERS,C.K.ROSS,I.KIRBY,P.H.RAY, REMARK 1 AUTH 2 J.E.WILSON,M.NORMAN,J.S.REN,R.M.ESNOUF,E.F.GARMAN, REMARK 1 AUTH 3 E.Y.JONES,D.I.STUART REMARK 1 TITL CRYSTALS OF HIV-1 REVERSE TRANSCRIPTASE REMARK 1 TITL 2 DIFFRACTING TO 2.2 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 242 586 1994 REMARK 1 REFN ISSN 0022-2836

REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 26069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.335 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1207 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2901 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 146 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 : 7830 REMARK 3 NUCLEIC ACID ATOMS : NULL REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.00 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.60 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.40 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) : 3.000 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 8.000 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 8.000 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 16.000; 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : UC38.PAR REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : UC38.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DUE TO THE LOW RATIO BETWEEN THE REMARK 3 NUMBER OF REFLECTIONS AND THE NUMBER OF PARAMETERS TO BE REMARK 3 REFINED, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS REMARK 3 ATOMS MORE THAN 25 ANGSTROM FROM THE CA ATOM OF TYR188) WERE REMARK 3 TIGHTLY RESTRAINED TO THEIR POSITION IN THE NINE-DOMAIN RIGID- REMARK 3 BODY REFINED MODEL OF RT-MKC-442 COMPLEX, AND STRONG REMARK 3 STEREOCHEMICAL RESTRAINTS WERE EMPLOYED IN THE REFINEMENT. THE REMARK 3 ABOVE THERMAL FACTOR AND RMS DEVIATIONS OF THE STEREOCHEMISTRY REMARK 3 ARE TAKEN FROM THE FINAL MODEL WHICH WAS REFINED USING THE REMARK 3 WHOLE DATA SET. THE FINAL R FACTOR FOR THE WHOLE DATA SET IS REMARK 3 0.234.

REMARK 4 REMARK 4 1RT6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX7.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26073 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 3.240 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.65 REMARK 200 R MERGE FOR SHELL (I) : 0.35700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.910 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: RT-MKC-442 COMPLEX (PDB ENTRY 1RT1) REMARK 200 REMARK 200 REMARK: ALL DATA INCLUDED APART FROM OUTLIERS

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.0

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 68.50000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.90000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.90000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 68.50000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.65000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL

REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.

REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 540 REMARK 465 GLY A 541 REMARK 465 ILE A 542 REMARK 465 GLY A 543 REMARK 465 GLY A 544 REMARK 465 ASN A 545 REMARK 465 GLU A 546 REMARK 465 GLN A 547 REMARK 465 VAL A 548 REMARK 465 ASP A 549 REMARK 465 LYS A 550 REMARK 465 LEU A 551 REMARK 465 VAL A 552 REMARK 465 SER A 553 REMARK 465 ALA A 554 REMARK 465 GLY A 555 REMARK 465 ILE A 556 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 GLU B 89 REMARK 465 VAL B 90 REMARK 465 GLN B 91 REMARK 465 LEU B 92 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 TYR B 232

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 14 N - CA - C ANGL. DEV. = 17.3 DEGREES REMARK 500 PRO A 14 C - N - CA ANGL. DEV. = 23.6 DEGREES REMARK 500 PRO A 14 C - N - CD ANGL. DEV. = -20.6 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 ILE A 2 -139.62 -108.69 REMARK 500 PRO A 4 51.18 -107.23 REMARK 500 LYS A 13 -80.79 17.78 REMARK 500 PRO A 14 151.32 -16.07 REMARK 500 ILE A 50 -160.22 -122.32 REMARK 500 ASP A 67 -34.76 -34.24 REMARK 500 SER A 68 -5.67 -143.60 REMARK 500 THR A 69 7.73 57.38 REMARK 500 ARG A 72 -160.37 -119.09 REMARK 500 GLN A 91 96.88 -52.50 REMARK 500 ASP A 121 97.62 -64.05 REMARK 500 GLU A 122 -41.43 -27.20 REMARK 500 ILE A 135 98.75 -57.21 REMARK 500 GLU A 138 -131.17 -84.67 REMARK 500 MET A 184 -131.99 57.04 REMARK 500 ILE A 195 -39.24 -37.07 REMARK 500 PRO A 217 -167.38 -46.73 REMARK 500 MET A 230 97.36 41.08 REMARK 500 PRO A 236 -17.55 -48.06 REMARK 500 ILE A 270 -74.02 -69.28 REMARK 500 ALA A 288 149.66 -172.77 REMARK 500 PRO A 345 129.29 -36.34 REMARK 500 PHE A 346 -2.71 64.89 REMARK 500 HIS A 361 124.53 -172.33 REMARK 500 TRP A 401 -70.93 -67.38 REMARK 500 PRO A 412 -170.51 -53.21 REMARK 500 PRO A 420 154.31 -45.63 REMARK 500 ASP A 471 65.12 61.36 REMARK 500 GLN A 509 54.43 39.88 REMARK 500 PRO B 9 88.78 -64.46 REMARK 500 PRO B 14 108.08 -36.99 REMARK 500 LYS B 66 -51.66 -5.95 REMARK 500 ASP B 67 -78.01 -101.49 REMARK 500 SER B 68 172.65 -50.48 REMARK 500 GLN B 85 153.26 -47.94 REMARK 500 PHE B 87 40.21 -105.71 REMARK 500 ASN B 136 19.50 54.69 REMARK 500 GLU B 169 -60.71 -24.99 REMARK 500 MET B 184 -111.59 49.32 REMARK 500 ILE B 195 -62.71 -25.97 REMARK 500 ARG B 211 37.45 -75.69 REMARK 500 TRP B 212 -54.78 -148.48 REMARK 500 HIS B 235 58.35 -149.26 REMARK 500 TRP B 239 -141.88 -104.56 REMARK 500 THR B 240 83.71 16.76 REMARK 500 VAL B 241 -153.14 -162.15 REMARK 500 GLN B 242 102.27 90.64 REMARK 500 GLN B 334 28.43 48.28 REMARK 500 PHE B 346 -12.46 72.72 REMARK 500 GLN B 407 -11.01 -147.38 REMARK 500 PRO B 421 -34.18 -36.08 REMARK 500 GLU B 438 107.27 -54.69 REMARK 500 THR B 439 79.22 -108.26 REMARK 500 REMARK 500 REMARK: NULL

REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1095 DISTANCE = 5.60 ANGSTROMS

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1000 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UC3 A 999

DBREF 1RT6 A 1 560 UNP P04585 POL_HV1H2 587 1146 DBREF 1RT6 B 1 440 UNP P04585 POL_HV1H2 587 1026

SEQADV 1RT6 CSD A 280 UNP P04585 CYS 435 MODIFIED RESIDUE

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 CSD 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

MODRES 1RT6 CSD A 280 CYS 3-SULFINOALANINE

HET CSD A 280 8 HET PO4 A1000 5 HET UC3 A 999 20

HETNAM CSD 3-SULFINOALANINE HETNAM PO4 PHOSPHATE ION HETNAM UC3 1-METHYL ETHYL 2-CHLORO-5-[[[(1-METHYLETHOXY) HETNAM 2 UC3 THIOOXO]METHYL]AMINO]-BENZOATE

HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE HETSYN UC3 UC38

FORMUL 1 CSD C3 H7 N O4 S FORMUL 3 PO4 O4 P 3- FORMUL 4 UC3 C14 H18 CL N O3 S FORMUL 5 HOH *96(H2 O)

HELIX 1 1 GLU A 28 GLU A 44 1 17 HELIX 2 2 ARG A 78 ARG A 83 1 6 HELIX 3 3 PRO A 97 GLY A 99 5 3 HELIX 4 4 TYR A 115 SER A 117 5 3 HELIX 5 5 PHE A 124 THR A 128 5 5 HELIX 6 6 SER A 156 ASN A 175 1 20 HELIX 7 7 ILE A 195 TRP A 212 1 18 HELIX 8 8 LYS A 219 HIS A 221 5 3 HELIX 9 9 VAL A 254 ILE A 270 1 17 HELIX 10 10 ARG A 277 LEU A 279 5 3 HELIX 11 11 GLU A 297 LYS A 311 1 15 HELIX 12 12 ASP A 364 TRP A 383 1 20 HELIX 13 13 LYS A 395 TRP A 402 1 8 HELIX 14 14 ASN A 474 ASP A 488 1 15 HELIX 15 15 GLN A 500 ALA A 508 1 9 HELIX 16 16 GLU A 516 LYS A 527 1 12 HELIX 17 17 GLU B 28 LYS B 43 1 16 HELIX 18 18 PHE B 77 ARG B 83 5 7 HELIX 19 19 ALA B 98 LYS B 102 5 5 HELIX 20 20 ASP B 113 SER B 117 5 5 HELIX 21 21 ARG B 125 THR B 128 5 4 HELIX 22 22 ILE B 135 ASN B 137 5 3 HELIX 23 23 LYS B 154 GLN B 174 1 21 HELIX 24 24 ILE B 195 LEU B 210 1 16 HELIX 25 25 PRO B 236 LYS B 238 5 3 HELIX 26 26 VAL B 254 GLN B 269 1 16 HELIX 27 27 ARG B 277 LEU B 282 1 6 HELIX 28 28 GLU B 297 LEU B 310 1 14 HELIX 29 29 ASP B 364 TRP B 383 1 20 HELIX 30 30 LYS B 395 TYR B 405 1 11 HELIX 31 31 PRO B 421 LEU B 429 1 9

SHEET 1 A 3 ILE A 47 LYS A 49 0 SHEET 2 A 3 ILE A 142 TYR A 146 -1 N GLN A 145 O 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 3 SER A 105 ASP A 110 0 SHEET 2 B 3 ASP A 186 SER A 191 -1 N SER A 191 O SER A 105 SHEET 3 B 3 ILE A 178 TYR A 183 -1 N TYR A 183 O ASP A 186 SHEET 1 C 3 PHE A 227 TRP A 229 0 SHEET 2 C 3 TYR A 232 HIS A 235 -1 N LEU A 234 O PHE A 227 SHEET 3 C 3 LYS A 238 VAL A 241 -1 N THR A 240 O GLU A 233 SHEET 1 D 5 TRP A 414 PHE A 416 0 SHEET 2 D 5 LYS A 388 LEU A 391 1 N PHE A 389 O GLU A 415 SHEET 3 D 5 ILE A 326 LYS A 331 1 N ALA A 327 O LYS A 388 SHEET 4 D 5 TRP A 337 TYR A 342 -1 N TYR A 342 O ILE A 326 SHEET 5 D 5 ASN A 348 TYR A 354 -1 N TYR A 354 O TRP A 337 SHEET 1 E 5 GLN A 464 THR A 470 0 SHEET 2 E 5 LEU A 452 THR A 459 -1 N TYR A 457 O LYS A 465 SHEET 3 E 5 GLU A 438 ASN A 447 -1 N ASN A 447 O LEU A 452 SHEET 4 E 5 GLU A 492 THR A 497 1 N ASN A 494 O GLU A 438 SHEET 5 E 5 LYS A 530 TRP A 535 1 N LYS A 530 O VAL A 493 SHEET 1 F 2 VAL B 60 LYS B 64 0 SHEET 2 F 2 TRP B 71 VAL B 75 -1 N LEU B 74 O PHE B 61 SHEET 1 G 3 SER B 105 ASP B 110 0 SHEET 2 G 3 ASP B 186 SER B 191 -1 N SER B 191 O SER B 105 SHEET 3 G 3 VAL B 179 TYR B 183 -1 N TYR B 183 O ASP B 186 SHEET 1 H 5 GLU B 413 PHE B 416 0 SHEET 2 H 5 LYS B 388 LEU B 391 1 N PHE B 389 O GLU B 413 SHEET 3 H 5 ILE B 326 GLY B 333 1 N ALA B 327 O LYS B 388 SHEET 4 H 5 GLN B 336 TYR B 342 -1 N TYR B 342 O ILE B 326 SHEET 5 H 5 ASN B 348 ALA B 355 -1 N TYR B 354 O TRP B 337

LINK N CSD A 280 C LEU A 279 1555 1555 1.34 LINK C CSD A 280 N LYS A 281 1555 1555 1.33

CISPEP 1 LYS A 13 PRO A 14 0 0.49 CISPEP 2 PRO A 225 PRO A 226 0 -0.15 CISPEP 3 PRO A 420 PRO A 421 0 0.11

SITE 1 AC1 6 ILE A 94 PRO A 95 HIS A 96 PRO A 97 SITE 2 AC1 6 TRP A 229 MET A 230 SITE 1 AC2 11 LEU A 100 LYS A 101 LYS A 103 VAL A 106 SITE 2 AC2 11 VAL A 179 TYR A 188 PHE A 227 TRP A 229 SITE 3 AC2 11 LEU A 234 TYR A 318 GLU B 138

CRYST1 137.000 109.300 71.800 90.00 90.00 90.00 P 21 21 21 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 0.007299 0.000000 0.000000 0.00000

SCALE2 0.000000 0.009149 0.000000 0.00000

SCALE3 0.000000 0.000000 0.013928 0.00000