HEADER TRANSFERASE 06-JAN-10 3LAN TITLE CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH N1- TITLE 2 BUTYL PYRIMIDINEDIONE NON-NUCLEOSIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV REVERSE TRANSCRIPTASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.7.49; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11706; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS HIV, REVERSE TRANSCRIPTASE, RT, NNRTI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.B.LANSDON,M.L.MITCHELL REVDAT 3 06-SEP-23 3LAN 1 REMARK REVDAT 2 09-MAR-10 3LAN 1 JRNL REVDAT 1 23-FEB-10 3LAN 0 JRNL AUTH M.L.MITCHELL,J.C.SON,H.GUO,Y.A.IM,E.J.CHO,J.WANG,J.HAYES, JRNL AUTH 2 M.WANG,A.PAUL,E.B.LANSDON,J.M.CHEN,D.GRAUPE,G.RHODES,G.X.HE, JRNL AUTH 3 R.GELEZIUNAS,L.XU,C.U.KIM JRNL TITL N1-ALKYL PYRIMIDINEDIONES AS NON-NUCLEOSIDE INHIBITORS OF JRNL TITL 2 HIV-1 REVERSE TRANSCRIPTASE. JRNL REF BIOORG.MED.CHEM.LETT. V. 20 1589 2010 JRNL REFN ISSN 0960-894X JRNL PMID 20138513 JRNL DOI 10.1016/J.BMCL.2010.01.085 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2005 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 153326.380 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 39668 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2730 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2710 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.314 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2144 REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : 0.0070 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 42848 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5167 REMARK 3 BIN R VALUE (WORKING SET) : 0.3880 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 268 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7842 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.33000 REMARK 3 B22 (A**2) : -11.78000 REMARK 3 B33 (A**2) : 20.11000 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) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.45 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.47 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.156 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.580 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.540 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.670 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.880 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.000 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 39.39 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 : PROTEIN_REP.P REMARK 3 PARAMETER FILE 2 : KBT.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PAR REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : KBT.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3LAN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000057042. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 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 : 43129 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.47900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1VRT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3M AMMONIUM SULFATE, 100MM REMARK 280 CACODYLATE, 5MM SODIUM MALONATE, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 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 76.80550 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 76.80550 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 59.35100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 77.01350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 59.35100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 77.01350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 76.80550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.35100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 77.01350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 76.80550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 59.35100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 77.01350 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: 6460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -101.0 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 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 LYS B 66 REMARK 465 ASP B 67 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 MET B 357 REMARK 465 ARG B 358 REMARK 465 GLY B 359 REMARK 465 ALA B 360 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 465 TYR B 441 REMARK 465 VAL B 442 REMARK 465 ASP B 443 REMARK 465 GLY B 444 REMARK 465 ALA B 445 REMARK 465 ALA B 446 REMARK 465 ASN B 447 REMARK 465 ARG B 448 REMARK 465 GLU B 449 REMARK 465 THR B 450 REMARK 465 LYS B 451 REMARK 465 LEU B 452 REMARK 465 GLY B 453 REMARK 465 LYS B 454 REMARK 465 ALA B 455 REMARK 465 GLY B 456 REMARK 465 TYR B 457 REMARK 465 VAL B 458 REMARK 465 THR B 459 REMARK 465 ASN B 460 REMARK 465 ARG B 461 REMARK 465 GLY B 462 REMARK 465 ARG B 463 REMARK 465 GLN B 464 REMARK 465 LYS B 465 REMARK 465 VAL B 466 REMARK 465 VAL B 467 REMARK 465 THR B 468 REMARK 465 LEU B 469 REMARK 465 THR B 470 REMARK 465 ASP B 471 REMARK 465 THR B 472 REMARK 465 THR B 473 REMARK 465 ASN B 474 REMARK 465 GLN B 475 REMARK 465 LYS B 476 REMARK 465 THR B 477 REMARK 465 GLU B 478 REMARK 465 LEU B 479 REMARK 465 GLN B 480 REMARK 465 ALA B 481 REMARK 465 ILE B 482 REMARK 465 TYR B 483 REMARK 465 LEU B 484 REMARK 465 ALA B 485 REMARK 465 LEU B 486 REMARK 465 GLN B 487 REMARK 465 ASP B 488 REMARK 465 SER B 489 REMARK 465 GLY B 490 REMARK 465 LEU B 491 REMARK 465 GLU B 492 REMARK 465 VAL B 493 REMARK 465 ASN B 494 REMARK 465 ILE B 495 REMARK 465 VAL B 496 REMARK 465 THR B 497 REMARK 465 ASP B 498 REMARK 465 SER B 499 REMARK 465 GLN B 500 REMARK 465 TYR B 501 REMARK 465 ALA B 502 REMARK 465 LEU B 503 REMARK 465 GLY B 504 REMARK 465 ILE B 505 REMARK 465 ILE B 506 REMARK 465 GLN B 507 REMARK 465 ALA B 508 REMARK 465 GLN B 509 REMARK 465 PRO B 510 REMARK 465 ASP B 511 REMARK 465 GLN B 512 REMARK 465 SER B 513 REMARK 465 GLU B 514 REMARK 465 SER B 515 REMARK 465 GLU B 516 REMARK 465 LEU B 517 REMARK 465 VAL B 518 REMARK 465 ASN B 519 REMARK 465 GLN B 520 REMARK 465 ILE B 521 REMARK 465 ILE B 522 REMARK 465 GLU B 523 REMARK 465 GLN B 524 REMARK 465 LEU B 525 REMARK 465 ILE B 526 REMARK 465 LYS B 527 REMARK 465 LYS B 528 REMARK 465 GLU B 529 REMARK 465 LYS B 530 REMARK 465 VAL B 531 REMARK 465 TYR B 532 REMARK 465 LEU B 533 REMARK 465 ALA B 534 REMARK 465 TRP B 535 REMARK 465 VAL B 536 REMARK 465 PRO B 537 REMARK 465 ALA B 538 REMARK 465 HIS B 539 REMARK 465 LYS B 540 REMARK 465 GLY B 541 REMARK 465 ILE B 542 REMARK 465 GLY B 543 REMARK 465 GLY B 544 REMARK 465 ASN B 545 REMARK 465 GLU B 546 REMARK 465 GLN B 547 REMARK 465 VAL B 548 REMARK 465 ASP B 549 REMARK 465 LYS B 550 REMARK 465 LEU B 551 REMARK 465 VAL B 552 REMARK 465 SER B 553 REMARK 465 ALA B 554 REMARK 465 GLY B 555 REMARK 465 ILE B 556 REMARK 465 ARG B 557 REMARK 465 LYS B 558 REMARK 465 VAL B 559 REMARK 465 LEU B 560 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 HIS B 361 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 54 105.34 -39.94 REMARK 500 LYS A 66 -132.78 33.10 REMARK 500 SER A 68 -171.36 -68.81 REMARK 500 ARG A 78 -50.05 -24.45 REMARK 500 GLN A 91 113.19 -177.55 REMARK 500 ASN A 136 6.18 52.61 REMARK 500 ASN A 137 -1.78 84.63 REMARK 500 MET A 184 -137.05 52.82 REMARK 500 LYS A 219 -14.00 -41.65 REMARK 500 TRP A 229 143.39 -174.89 REMARK 500 MET A 230 32.90 30.96 REMARK 500 ILE A 270 -24.19 -142.62 REMARK 500 GLN A 334 86.54 -69.53 REMARK 500 PHE A 346 52.80 -113.34 REMARK 500 ARG A 356 145.49 -38.00 REMARK 500 TRP A 410 133.09 176.80 REMARK 500 PRO A 412 -175.55 -63.30 REMARK 500 ASP A 471 79.27 49.38 REMARK 500 ASP A 511 12.50 -140.30 REMARK 500 THR B 69 59.11 -110.55 REMARK 500 LEU B 92 -148.33 -118.94 REMARK 500 MET B 184 -127.39 50.03 REMARK 500 LEU B 214 70.97 -117.29 REMARK 500 PRO B 247 173.53 -57.11 REMARK 500 ASP B 250 -60.40 -90.20 REMARK 500 THR B 362 50.02 -65.42 REMARK 500 GLN B 428 -173.60 -64.41 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 PRO A 52 GLU A 53 62.31 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 KBT A 561 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 562 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 563 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 564 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 565 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 561 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 562 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LAK RELATED DB: PDB REMARK 900 RELATED ID: 3LAL RELATED DB: PDB REMARK 900 RELATED ID: 3LAM RELATED DB: PDB DBREF 3LAN A 1 560 UNP P04585 POL_HV1H2 588 1147 DBREF 3LAN B 1 560 UNP P04585 POL_HV1H2 588 1147 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 CYS 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 560 PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS LEU LYS SEQRES 2 B 560 PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP PRO LEU SEQRES 3 B 560 THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE CYS THR SEQRES 4 B 560 GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE GLY PRO SEQRES 5 B 560 GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE LYS LYS SEQRES 6 B 560 LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP PHE ARG SEQRES 7 B 560 GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU VAL GLN SEQRES 8 B 560 LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS LYS LYS SEQRES 9 B 560 SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR PHE SER SEQRES 10 B 560 VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR ALA PHE SEQRES 11 B 560 THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY ILE ARG SEQRES 12 B 560 TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS GLY SER SEQRES 13 B 560 PRO ALA ILE PHE GLN SER SER MET THR LYS ILE LEU GLU SEQRES 14 B 560 PRO PHE ARG LYS GLN ASN PRO ASP ILE VAL ILE TYR GLN SEQRES 15 B 560 TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU GLU ILE SEQRES 16 B 560 GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG GLN HIS SEQRES 17 B 560 LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS LYS HIS SEQRES 18 B 560 GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR GLU LEU SEQRES 19 B 560 HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL LEU PRO SEQRES 20 B 560 GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN LYS LEU SEQRES 21 B 560 VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR PRO GLY SEQRES 22 B 560 ILE LYS VAL ARG GLN LEU CYS LYS LEU LEU ARG GLY THR SEQRES 23 B 560 LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU GLU ALA SEQRES 24 B 560 GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU LYS GLU SEQRES 25 B 560 PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS ASP LEU SEQRES 26 B 560 ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN TRP THR SEQRES 27 B 560 TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU LYS THR SEQRES 28 B 560 GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR ASN ASP SEQRES 29 B 560 VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE THR THR SEQRES 30 B 560 GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS PHE LYS SEQRES 31 B 560 LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP TRP THR SEQRES 32 B 560 GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP GLU PHE SEQRES 33 B 560 VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR GLN LEU SEQRES 34 B 560 GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE TYR VAL SEQRES 35 B 560 ASP GLY ALA ALA ASN ARG GLU THR LYS LEU GLY LYS ALA SEQRES 36 B 560 GLY TYR VAL THR ASN ARG GLY ARG GLN LYS VAL VAL THR SEQRES 37 B 560 LEU THR ASP THR THR ASN GLN LYS THR GLU LEU GLN ALA SEQRES 38 B 560 ILE TYR LEU ALA LEU GLN ASP SER GLY LEU GLU VAL ASN SEQRES 39 B 560 ILE VAL THR ASP SER GLN TYR ALA LEU GLY ILE ILE GLN SEQRES 40 B 560 ALA GLN PRO ASP GLN SER GLU SER GLU LEU VAL ASN GLN SEQRES 41 B 560 ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS VAL TYR LEU SEQRES 42 B 560 ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY GLY ASN GLU SEQRES 43 B 560 GLN VAL ASP LYS LEU VAL SER ALA GLY ILE ARG LYS VAL SEQRES 44 B 560 LEU HET KBT A 561 26 HET SO4 A 562 5 HET SO4 A 563 5 HET SO4 A 564 5 HET SO4 A 565 5 HET SO4 B 561 5 HET SO4 B 562 5 HETNAM KBT 3-{[3-BUTYL-5-(1-METHYLETHYL)-2,6-DIOXO-1,2,3,6- HETNAM 2 KBT TETRAHYDROPYRIMIDIN-4-YL]CARBONYL}-5- HETNAM 3 KBT METHYLBENZONITRILE HETNAM SO4 SULFATE ION FORMUL 3 KBT C20 H23 N3 O3 FORMUL 4 SO4 6(O4 S 2-) FORMUL 10 HOH *104(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 SER A 134 GLU A 138 5 5 HELIX 7 7 GLY A 155 ASN A 175 1 21 HELIX 8 8 GLU A 194 TRP A 212 1 19 HELIX 9 9 VAL A 254 SER A 268 1 15 HELIX 10 10 VAL A 276 LYS A 281 1 6 HELIX 11 11 LEU A 282 ARG A 284 5 3 HELIX 12 12 THR A 296 GLU A 312 1 17 HELIX 13 13 ASN A 363 GLY A 384 1 22 HELIX 14 14 GLN A 394 TYR A 405 1 12 HELIX 15 15 GLN A 475 ASP A 488 1 14 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 ILE A 542 VAL A 552 1 11 HELIX 19 19 THR B 27 GLU B 44 1 18 HELIX 20 20 PHE B 77 VAL B 90 1 14 HELIX 21 21 GLY B 99 LYS B 103 5 5 HELIX 22 22 GLY B 112 VAL B 118 5 7 HELIX 23 23 PHE B 124 ALA B 129 5 6 HELIX 24 24 SER B 134 GLU B 138 5 5 HELIX 25 25 LYS B 154 ASN B 175 1 22 HELIX 26 26 GLU B 194 ARG B 211 1 18 HELIX 27 27 HIS B 235 TRP B 239 5 5 HELIX 28 28 THR B 253 SER B 268 1 16 HELIX 29 29 VAL B 276 LYS B 281 1 6 HELIX 30 30 THR B 296 GLU B 312 1 17 HELIX 31 31 ASN B 363 GLY B 384 1 22 HELIX 32 32 GLN B 394 TRP B 402 1 9 HELIX 33 33 THR B 403 TYR B 405 5 3 HELIX 34 34 PRO B 420 TYR B 427 1 8 SHEET 1 A 3 ILE A 47 ILE A 50 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 VAL A 189 N THR A 107 SHEET 3 C 3 VAL A 179 TYR A 183 -1 N VAL A 179 O GLY A 190 SHEET 1 D 3 PHE A 227 TRP A 229 0 SHEET 2 D 3 TYR A 232 LEU A 234 -1 O 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 2 TRP A 252 THR A 253 0 SHEET 2 E 2 VAL A 292 ILE A 293 -1 O ILE A 293 N TRP A 252 SHEET 1 F 5 LYS A 347 TYR A 354 0 SHEET 2 F 5 TRP A 337 GLU A 344 -1 N ILE A 341 O LEU A 349 SHEET 3 F 5 ILE A 326 LYS A 331 -1 N GLN A 330 O THR A 338 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 O GLU A 415 N LEU A 391 SHEET 1 G 2 HIS A 361 THR A 362 0 SHEET 2 G 2 GLN A 512 SER A 513 -1 O GLN A 512 N THR A 362 SHEET 1 H 5 GLN A 464 THR A 470 0 SHEET 2 H 5 LEU A 452 THR A 459 -1 N GLY A 453 O LEU A 469 SHEET 3 H 5 THR A 439 ALA A 446 -1 N TYR A 441 O VAL A 458 SHEET 4 H 5 GLU A 492 THR A 497 1 O VAL A 496 N PHE A 440 SHEET 5 H 5 LYS A 530 TRP A 535 1 O TYR A 532 N ILE A 495 SHEET 1 I 3 ILE B 47 LYS B 49 0 SHEET 2 I 3 ILE B 142 TYR B 146 -1 O GLN B 145 N SER B 48 SHEET 3 I 3 PHE B 130 ILE B 132 -1 N ILE B 132 O ILE B 142 SHEET 1 J 2 VAL B 60 ILE B 63 0 SHEET 2 J 2 ARG B 72 VAL B 75 -1 O LEU B 74 N PHE B 61 SHEET 1 K 4 VAL B 179 TYR B 183 0 SHEET 2 K 4 ASP B 186 SER B 191 -1 O GLY B 190 N VAL B 179 SHEET 3 K 4 SER B 105 ASP B 110 -1 N LEU B 109 O LEU B 187 SHEET 4 K 4 GLU B 233 LEU B 234 -1 O LEU B 234 N VAL B 106 SHEET 1 L 5 ASN B 348 ALA B 355 0 SHEET 2 L 5 GLN B 336 TYR B 342 -1 N ILE B 341 O LYS B 350 SHEET 3 L 5 ILE B 326 GLY B 333 -1 N GLN B 330 O THR B 338 SHEET 4 L 5 LYS B 388 LEU B 391 1 O LYS B 390 N ALA B 327 SHEET 5 L 5 TRP B 414 PHE B 416 1 O GLU B 415 N PHE B 389 CISPEP 1 PRO A 225 PRO A 226 0 4.60 CISPEP 2 PRO A 345 PHE A 346 0 -10.61 CISPEP 3 PRO A 420 PRO A 421 0 0.29 SITE 1 AC1 14 LEU A 100 LYS A 101 LYS A 103 TYR A 181 SITE 2 AC1 14 TYR A 188 VAL A 189 GLY A 190 PHE A 227 SITE 3 AC1 14 TRP A 229 LEU A 234 HIS A 235 PRO A 236 SITE 4 AC1 14 TYR A 318 HOH A 586 SITE 1 AC2 7 ARG A 211 GLY A 436 ALA A 437 GLU A 438 SITE 2 AC2 7 ASN A 460 ARG A 461 ALA B 288 SITE 1 AC3 3 GLY A 436 ARG A 461 HOH A 568 SITE 1 AC4 4 ARG A 211 ASN A 460 THR B 286 ALA B 288 SITE 1 AC5 3 SER A 515 GLU A 516 LEU A 517 SITE 1 AC6 4 LYS A 11 PRO B 55 TYR B 56 LYS B 126 SITE 1 AC7 3 LEU B 234 HIS B 235 TRP B 239 CRYST1 118.702 154.027 153.611 90.00 90.00 90.00 C 2 2 21 16 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 0.008424 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006510 0.00000