HEADER HYDROLASE/HYDROLASE INHIBITOR 17-SEP-12 4H4O TITLE CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH TITLE 2 (E)-3-(3-(2-(2-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)ETHOXY)- 4- TITLE 3 FLUOROPHENOXY)-5-FLUOROPHENYL)ACRYLONITRILE (JLJ506), A NON- TITLE 4 NUCLEOSIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: REVERSE TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEASE H, COMPND 3 P66 RT; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT; COMPND 6 SYNONYM: GAG-POL POLYPROTEIN; COMPND 7 EC: 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: REVERSE TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEASE H, COMPND 12 P51 RT; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT; COMPND 15 SYNONYM: GAG-POL POLYPROTEIN; COMPND 16 EC: 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2; COMPND 17 ENGINEERED: YES; COMPND 18 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 BH10; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11678; SOURCE 5 STRAIN: BH10 ISOLATE; SOURCE 6 GENE: P66 RT; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCDF-2; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 14 ORGANISM_COMMON: HIV-1; SOURCE 15 ORGANISM_TAXID: 11678; SOURCE 16 STRAIN: BH10 ISOLATE; SOURCE 17 GENE: P51 RT; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PCDF-2 KEYWDS POLYMERASE, TRANSFERASE, HYDROLASE/INHIBITOR, RNASE, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.M.FREY,K.S.ANDERSON REVDAT 4 20-SEP-23 4H4O 1 REMARK SEQADV REVDAT 3 15-NOV-17 4H4O 1 REMARK REVDAT 2 02-JAN-13 4H4O 1 JRNL REVDAT 1 05-DEC-12 4H4O 0 JRNL AUTH K.M.FREY,M.BOLLINI,A.C.MISLAK,J.A.CISNEROS, JRNL AUTH 2 R.GALLARDO-MACIAS,W.L.JORGENSEN,K.S.ANDERSON JRNL TITL CRYSTAL STRUCTURES OF HIV-1 REVERSE TRANSCRIPTASE WITH JRNL TITL 2 PICOMOLAR INHIBITORS REVEAL KEY INTERACTIONS FOR DRUG JRNL TITL 3 DESIGN. JRNL REF J.AM.CHEM.SOC. V. 134 19501 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 23163887 JRNL DOI 10.1021/JA3092642 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD (ML) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.890 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34760 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.750 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 41.7264 - 6.9749 0.99 2400 146 0.2004 0.2094 REMARK 3 2 6.9749 - 5.5403 1.00 2393 146 0.2424 0.2629 REMARK 3 3 5.5403 - 4.8411 1.00 2359 145 0.2121 0.2620 REMARK 3 4 4.8411 - 4.3990 1.00 2349 144 0.2011 0.2396 REMARK 3 5 4.3990 - 4.0840 1.00 2339 142 0.2060 0.2302 REMARK 3 6 4.0840 - 3.8434 1.00 2338 142 0.2310 0.2912 REMARK 3 7 3.8434 - 3.6510 1.00 2339 144 0.2515 0.2856 REMARK 3 8 3.6510 - 3.4922 1.00 2329 141 0.2636 0.2941 REMARK 3 9 3.4922 - 3.3578 1.00 2354 144 0.2611 0.3116 REMARK 3 10 3.3578 - 3.2420 1.00 2342 143 0.2804 0.2848 REMARK 3 11 3.2420 - 3.1407 1.00 2294 140 0.2726 0.3666 REMARK 3 12 3.1407 - 3.0509 1.00 2334 141 0.2984 0.3737 REMARK 3 13 3.0509 - 2.9706 1.00 2339 143 0.3176 0.3540 REMARK 3 14 2.9706 - 2.8982 0.98 2252 138 0.3317 0.3640 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 79.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 164.0 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 8258 REMARK 3 ANGLE : 0.876 11226 REMARK 3 CHIRALITY : 0.065 1211 REMARK 3 PLANARITY : 0.004 1413 REMARK 3 DIHEDRAL : 13.534 3137 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4H4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000075014. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : CRYOGENICALLY COOLED DOUBLE REMARK 200 CRYSTAL MONOCHROMETER WITH REMARK 200 HORIZONTAL FOCUSING SAGITTAL REMARK 200 BEND SECOND MONO CRYSTAL WITH 4: REMARK 200 1 MAGNIFICATION RATIO AND REMARK 200 VERTICALLY FOCUSING MIRROR. REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34778 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 41.722 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.59600 REMARK 200 R SYM FOR SHELL (I) : 0.47000 REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB CODE 1S9E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 8000, 100 MM AMMONIUM REMARK 280 SULFATE, 15 MM MAGNESIUM SULFATE, 5 MM SPERMINE-HCL, 50 MM HEPES REMARK 280 PH 5.5, 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 112.72550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.78750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 112.72550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.78750 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: 4850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 MET A -1 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASN B 137 O HOH B 505 2.15 REMARK 500 NE2 GLN A 91 O HOH B 505 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 718 O HOH A 718 2756 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 B 97 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 PRO B 421 C - N - CA ANGL. DEV. = 13.6 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 PRO A 4 49.72 -90.30 REMARK 500 LEU A 26 -68.60 -133.06 REMARK 500 ASN A 54 56.07 31.47 REMARK 500 ASP A 67 76.76 58.54 REMARK 500 SER A 68 -3.60 -59.65 REMARK 500 VAL A 90 -77.82 -82.14 REMARK 500 LEU A 92 -73.84 -63.77 REMARK 500 ASN A 136 -146.44 45.32 REMARK 500 ASN A 137 24.03 42.81 REMARK 500 GLU A 138 38.42 39.81 REMARK 500 MET A 184 -119.37 53.08 REMARK 500 LYS A 220 -88.86 59.90 REMARK 500 HIS A 221 0.63 108.95 REMARK 500 GLN A 222 -113.84 57.42 REMARK 500 PHE A 227 64.02 62.27 REMARK 500 ILE A 270 -58.76 -125.32 REMARK 500 THR A 286 -8.23 -54.56 REMARK 500 GLN A 343 -52.82 -127.68 REMARK 500 PRO A 412 -171.08 -69.81 REMARK 500 LEU A 452 -77.14 -83.06 REMARK 500 HIS A 539 -5.14 67.59 REMARK 500 ILE A 542 -75.24 -58.70 REMARK 500 GLU B 6 -73.86 -78.51 REMARK 500 LYS B 65 -73.47 -48.65 REMARK 500 LYS B 66 -79.53 -126.83 REMARK 500 THR B 84 -64.52 -130.33 REMARK 500 GLU B 89 -53.71 -143.99 REMARK 500 MET B 184 -118.89 53.00 REMARK 500 GLN B 222 -124.46 68.80 REMARK 500 ILE B 270 -62.62 -99.72 REMARK 500 PHE B 346 -4.97 69.85 REMARK 500 ARG B 356 -71.32 -62.00 REMARK 500 ALA B 360 19.63 58.29 REMARK 500 HIS B 361 -63.69 -135.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 220 HIS A 221 -139.98 REMARK 500 THR B 419 PRO B 420 -147.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 506 A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4H4M RELATED DB: PDB REMARK 900 RELATED ID: 2ZD1 RELATED DB: PDB REMARK 900 RELATED ID: 1S9E RELATED DB: PDB REMARK 900 RELATED ID: 2BE2 RELATED DB: PDB DBREF 4H4O A 1 555 UNP P03366 POL_HV1B1 600 1154 DBREF 4H4O B 1 428 UNP P03366 POL_HV1B1 600 1027 SEQADV 4H4O MET A -1 UNP P03366 INITIATING METHIONINE SEQADV 4H4O VAL A 0 UNP P03366 EXPRESSION TAG SEQADV 4H4O ALA A 172 UNP P03366 LYS 771 ENGINEERED MUTATION SEQADV 4H4O ALA A 173 UNP P03366 LYS 772 ENGINEERED MUTATION SEQADV 4H4O SER A 280 UNP P03366 CYS 879 ENGINEERED MUTATION SEQADV 4H4O SER B 280 UNP P03366 CYS 879 ENGINEERED MUTATION SEQRES 1 A 557 MET VAL PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS SEQRES 2 A 557 LEU LYS PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP SEQRES 3 A 557 PRO LEU THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE SEQRES 4 A 557 CYS THR GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE SEQRES 5 A 557 GLY PRO GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE SEQRES 6 A 557 LYS LYS LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP SEQRES 7 A 557 PHE ARG GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU SEQRES 8 A 557 VAL GLN LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS SEQRES 9 A 557 LYS LYS SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR SEQRES 10 A 557 PHE SER VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR SEQRES 11 A 557 ALA PHE THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY SEQRES 12 A 557 ILE ARG TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS SEQRES 13 A 557 GLY SER PRO ALA ILE PHE GLN SER SER MET THR LYS ILE SEQRES 14 A 557 LEU GLU PRO PHE ALA ALA GLN ASN PRO ASP ILE VAL ILE SEQRES 15 A 557 TYR GLN TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU SEQRES 16 A 557 GLU ILE GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG SEQRES 17 A 557 GLN HIS LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS SEQRES 18 A 557 LYS HIS GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR SEQRES 19 A 557 GLU LEU HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL SEQRES 20 A 557 LEU PRO GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN SEQRES 21 A 557 LYS LEU VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR SEQRES 22 A 557 PRO GLY ILE LYS VAL ARG GLN LEU SER LYS LEU LEU ARG SEQRES 23 A 557 GLY THR LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU SEQRES 24 A 557 GLU ALA GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU SEQRES 25 A 557 LYS GLU PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS SEQRES 26 A 557 ASP LEU ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN SEQRES 27 A 557 TRP THR TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU SEQRES 28 A 557 LYS THR GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR SEQRES 29 A 557 ASN ASP VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE SEQRES 30 A 557 THR THR GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS SEQRES 31 A 557 PHE LYS LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP SEQRES 32 A 557 TRP THR GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP SEQRES 33 A 557 GLU PHE VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR SEQRES 34 A 557 GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE SEQRES 35 A 557 TYR VAL ASP GLY ALA ALA ASN ARG GLU THR LYS LEU GLY SEQRES 36 A 557 LYS ALA GLY TYR VAL THR ASN LYS GLY ARG GLN LYS VAL SEQRES 37 A 557 VAL PRO LEU THR ASN THR THR ASN GLN LYS THR GLU LEU SEQRES 38 A 557 GLN ALA ILE TYR LEU ALA LEU GLN ASP SER GLY LEU GLU SEQRES 39 A 557 VAL ASN ILE VAL THR ASP SER GLN TYR ALA LEU GLY ILE SEQRES 40 A 557 ILE GLN ALA GLN PRO ASP LYS SER GLU SER GLU LEU VAL SEQRES 41 A 557 ASN GLN ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS VAL SEQRES 42 A 557 TYR LEU ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY GLY SEQRES 43 A 557 ASN GLU GLN VAL ASP LYS LEU VAL SER ALA GLY SEQRES 1 B 428 PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS LEU LYS SEQRES 2 B 428 PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP PRO LEU SEQRES 3 B 428 THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE CYS THR SEQRES 4 B 428 GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE GLY PRO SEQRES 5 B 428 GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE LYS LYS SEQRES 6 B 428 LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP PHE ARG SEQRES 7 B 428 GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU VAL GLN SEQRES 8 B 428 LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS LYS LYS SEQRES 9 B 428 SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR PHE SER SEQRES 10 B 428 VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR ALA PHE SEQRES 11 B 428 THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY ILE ARG SEQRES 12 B 428 TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS GLY SER SEQRES 13 B 428 PRO ALA ILE PHE GLN SER SER MET THR LYS ILE LEU GLU SEQRES 14 B 428 PRO PHE LYS LYS GLN ASN PRO ASP ILE VAL ILE TYR GLN SEQRES 15 B 428 TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU GLU ILE SEQRES 16 B 428 GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG GLN HIS SEQRES 17 B 428 LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS LYS HIS SEQRES 18 B 428 GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR GLU LEU SEQRES 19 B 428 HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL LEU PRO SEQRES 20 B 428 GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN LYS LEU SEQRES 21 B 428 VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR PRO GLY SEQRES 22 B 428 ILE LYS VAL ARG GLN LEU SER LYS LEU LEU ARG GLY THR SEQRES 23 B 428 LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU GLU ALA SEQRES 24 B 428 GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU LYS GLU SEQRES 25 B 428 PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS ASP LEU SEQRES 26 B 428 ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN TRP THR SEQRES 27 B 428 TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU LYS THR SEQRES 28 B 428 GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR ASN ASP SEQRES 29 B 428 VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE THR THR SEQRES 30 B 428 GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS PHE LYS SEQRES 31 B 428 LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP TRP THR SEQRES 32 B 428 GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP GLU PHE SEQRES 33 B 428 VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR GLN HET 506 A 601 30 HETNAM 506 (2E)-3-(3-{2-[2-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)- HETNAM 2 506 YL)ETHOXY]-4-FLUOROPHENOXY}-5-FLUOROPHENYL)PROP-2- HETNAM 3 506 ENENITRILE FORMUL 3 506 C21 H15 F2 N3 O4 FORMUL 4 HOH *49(H2 O) HELIX 1 1 THR A 27 GLU A 44 1 18 HELIX 2 2 PHE A 77 THR A 84 1 8 HELIX 3 3 HIS A 96 LEU A 100 5 5 HELIX 4 4 ALA A 114 VAL A 118 5 5 HELIX 5 5 ASP A 121 ALA A 129 5 9 HELIX 6 6 GLY A 155 ASN A 175 1 21 HELIX 7 7 GLU A 194 TRP A 212 1 19 HELIX 8 8 THR A 253 GLN A 269 1 17 HELIX 9 9 VAL A 276 LEU A 282 1 7 HELIX 10 10 LEU A 283 GLY A 285 5 3 HELIX 11 11 THR A 296 LEU A 310 1 15 HELIX 12 12 ASN A 363 GLY A 384 1 22 HELIX 13 13 GLN A 394 TYR A 405 1 12 HELIX 14 14 THR A 473 SER A 489 1 17 HELIX 15 15 SER A 499 ALA A 508 1 10 HELIX 16 16 SER A 515 LYS A 528 1 14 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 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 TRP B 212 1 19 HELIX 25 25 HIS B 235 TRP B 239 5 5 HELIX 26 26 THR B 253 SER B 268 1 16 HELIX 27 27 VAL B 276 LYS B 281 1 6 HELIX 28 28 LEU B 282 ARG B 284 5 3 HELIX 29 29 THR B 296 LYS B 311 1 16 HELIX 30 30 ASN B 363 GLY B 384 1 22 HELIX 31 31 GLN B 394 TRP B 402 1 9 HELIX 32 32 THR B 403 TYR B 405 5 3 HELIX 33 33 PRO B 421 GLN B 428 5 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 LYS A 64 0 SHEET 2 B 2 TRP A 71 VAL A 75 -1 O LEU A 74 N PHE A 61 SHEET 1 C 3 SER A 105 ASP A 110 0 SHEET 2 C 3 ASP A 186 SER A 191 -1 O LEU A 187 N LEU A 109 SHEET 3 C 3 ILE A 178 TYR A 183 -1 N TYR A 181 O TYR A 188 SHEET 1 D 3 LEU A 228 TRP A 229 0 SHEET 2 D 3 TYR A 232 LEU A 234 -1 O TYR A 232 N TRP A 229 SHEET 3 D 3 TRP A 239 VAL A 241 -1 O THR A 240 N GLU A 233 SHEET 1 E 5 LYS A 350 ALA A 355 0 SHEET 2 E 5 GLN A 336 TYR A 342 -1 N ILE A 341 O LYS A 350 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 LYS A 512 SER A 513 -1 O LYS A 512 N THR A 362 SHEET 1 G 5 GLN A 464 PRO A 468 0 SHEET 2 G 5 LYS A 454 THR A 459 -1 N ALA A 455 O VAL A 467 SHEET 3 G 5 GLU A 438 ALA A 445 -1 N ASP A 443 O GLY A 456 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 LYS B 64 0 SHEET 2 I 2 TRP B 71 VAL B 75 -1 O ARG B 72 N ILE B 63 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 GLU B 233 LEU B 234 -1 O LEU B 234 N VAL B 106 SHEET 1 K 5 ASN B 348 ALA B 355 0 SHEET 2 K 5 GLN B 336 TYR B 342 -1 N ILE B 341 O LYS B 350 SHEET 3 K 5 ILE B 326 GLY B 333 -1 N GLN B 330 O THR B 338 SHEET 4 K 5 LYS B 388 LEU B 391 1 O LYS B 390 N ALA B 327 SHEET 5 K 5 GLU B 413 PHE B 416 1 O GLU B 415 N LEU B 391 CISPEP 1 PRO A 25 LEU A 26 0 -4.88 CISPEP 2 PRO A 225 PRO A 226 0 -7.50 CISPEP 3 PRO A 226 PHE A 227 0 21.15 CISPEP 4 PRO A 420 PRO A 421 0 2.52 SITE 1 AC1 14 PRO A 95 LEU A 100 LYS A 101 LYS A 102 SITE 2 AC1 14 LYS A 103 VAL A 106 VAL A 108 VAL A 179 SITE 3 AC1 14 TYR A 188 GLY A 190 TRP A 229 LEU A 234 SITE 4 AC1 14 PRO A 236 TYR A 318 CRYST1 225.451 69.575 104.401 90.00 106.21 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 0.004436 0.000000 0.001289 0.00000 SCALE2 0.000000 0.014373 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009975 0.00000