HEADER ASPARTYL PROTEASE 16-JAN-96 1BVE TITLE HIV-1 PROTEASE-DMP323 COMPLEX IN SOLUTION, NMR, 28 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 STRAIN: HXB2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS AIDS, POLYPROTEIN, HYDROLASE, ASPARTYL PROTEASE, ENDONUCLEASE, RNA- KEYWDS 2 DIRECTED DNA POLYMERASE EXPDTA SOLUTION NMR NUMMDL 28 AUTHOR T.YAMAZAKI,A.P.HINCK,Y.-X.WANG,L.K.NICHOLSON,D.A.TORCHIA,P.WINGFIELD, AUTHOR 2 S.J.STAHL,J.D.KAUFMAN,C.CHANG,P.J.DOMAILLE,P.Y.S.LAM REVDAT 3 03-NOV-21 1BVE 1 COMPND REMARK SEQADV HETNAM REVDAT 2 24-FEB-09 1BVE 1 VERSN REVDAT 1 17-AUG-96 1BVE 0 JRNL AUTH T.YAMAZAKI,A.P.HINCK,Y.X.WANG,L.K.NICHOLSON,D.A.TORCHIA, JRNL AUTH 2 P.WINGFIELD,S.J.STAHL,J.D.KAUFMAN,C.H.CHANG,P.J.DOMAILLE, JRNL AUTH 3 P.Y.LAM JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE HIV-1 PROTEASE JRNL TITL 2 COMPLEXED WITH DMP323, A NOVEL CYCLIC UREA-TYPE INHIBITOR, JRNL TITL 3 DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY. JRNL REF PROTEIN SCI. V. 5 495 1996 JRNL REFN ISSN 0961-8368 JRNL PMID 8868486 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BVE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172109. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR 3.1 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 28 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 28 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS ENTRY CONTAINS 1 TO 28 OF 28 MODELS. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 1 LEU A 5 39.33 -89.56 REMARK 500 1 TRP A 6 59.36 16.28 REMARK 500 1 LEU A 24 95.17 -44.95 REMARK 500 1 GLU A 34 170.68 -45.16 REMARK 500 1 MET A 36 -158.92 -177.80 REMARK 500 1 ARG A 41 44.33 150.04 REMARK 500 1 GLN A 58 94.54 -54.58 REMARK 500 1 GLN A 61 63.48 69.48 REMARK 500 1 LEU A 63 82.91 -64.77 REMARK 500 1 PRO A 79 43.26 -80.31 REMARK 500 1 THR B 4 -105.19 -67.79 REMARK 500 1 LEU B 5 -11.64 -171.88 REMARK 500 1 THR B 12 90.50 -68.26 REMARK 500 1 GLU B 34 153.30 -36.56 REMARK 500 1 MET B 36 -174.12 -177.26 REMARK 500 1 GLN B 58 95.05 -48.02 REMARK 500 1 GLN B 61 59.27 84.95 REMARK 500 1 ALA B 71 100.88 -160.13 REMARK 500 1 PRO B 79 41.86 -81.44 REMARK 500 2 THR A 4 -90.91 -127.71 REMARK 500 2 LEU A 5 29.17 41.63 REMARK 500 2 TRP A 6 51.84 18.07 REMARK 500 2 LEU A 24 96.81 -43.94 REMARK 500 2 LEU A 33 116.35 -169.15 REMARK 500 2 GLU A 34 162.02 -39.35 REMARK 500 2 GLU A 35 156.85 -41.34 REMARK 500 2 MET A 36 -176.94 -179.02 REMARK 500 2 PRO A 39 -163.06 -69.53 REMARK 500 2 ARG A 41 50.44 -109.56 REMARK 500 2 GLN A 58 105.08 -55.06 REMARK 500 2 GLN A 61 61.91 78.29 REMARK 500 2 CYS A 67 38.23 36.93 REMARK 500 2 PRO A 79 39.86 -80.80 REMARK 500 2 THR B 4 32.51 -142.46 REMARK 500 2 LEU B 5 49.05 -85.55 REMARK 500 2 TRP B 6 52.57 17.84 REMARK 500 2 LEU B 24 103.90 -52.45 REMARK 500 2 ASP B 25 77.96 -101.16 REMARK 500 2 GLU B 34 166.69 -43.50 REMARK 500 2 GLN B 58 99.28 -48.42 REMARK 500 2 GLN B 61 63.77 71.49 REMARK 500 2 LEU B 63 85.71 -65.39 REMARK 500 2 PRO B 79 41.10 -79.57 REMARK 500 2 PRO B 81 21.52 -78.50 REMARK 500 3 GLN A 7 -99.04 -166.35 REMARK 500 3 LEU A 24 107.23 -46.86 REMARK 500 3 GLU A 34 153.34 -42.41 REMARK 500 3 GLN A 58 99.57 -60.67 REMARK 500 3 GLN A 61 60.33 82.01 REMARK 500 3 ALA A 71 99.72 -160.88 REMARK 500 REMARK 500 THIS ENTRY HAS 594 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 1 ARG A 8 0.18 SIDE CHAIN REMARK 500 1 ARG A 41 0.32 SIDE CHAIN REMARK 500 1 ARG A 57 0.28 SIDE CHAIN REMARK 500 1 ARG A 87 0.28 SIDE CHAIN REMARK 500 1 ARG B 8 0.27 SIDE CHAIN REMARK 500 1 ARG B 41 0.31 SIDE CHAIN REMARK 500 1 ARG B 57 0.31 SIDE CHAIN REMARK 500 1 ARG B 87 0.29 SIDE CHAIN REMARK 500 2 ARG A 8 0.32 SIDE CHAIN REMARK 500 2 ARG A 41 0.18 SIDE CHAIN REMARK 500 2 ARG A 57 0.23 SIDE CHAIN REMARK 500 2 ARG A 87 0.32 SIDE CHAIN REMARK 500 2 ARG B 8 0.29 SIDE CHAIN REMARK 500 2 ARG B 41 0.19 SIDE CHAIN REMARK 500 2 ARG B 87 0.18 SIDE CHAIN REMARK 500 3 ARG A 8 0.28 SIDE CHAIN REMARK 500 3 ARG A 41 0.26 SIDE CHAIN REMARK 500 3 ARG A 57 0.24 SIDE CHAIN REMARK 500 3 ARG A 87 0.29 SIDE CHAIN REMARK 500 3 ARG B 8 0.25 SIDE CHAIN REMARK 500 3 ARG B 41 0.20 SIDE CHAIN REMARK 500 3 ARG B 57 0.22 SIDE CHAIN REMARK 500 3 ARG B 87 0.12 SIDE CHAIN REMARK 500 4 ARG A 8 0.21 SIDE CHAIN REMARK 500 4 ARG A 41 0.29 SIDE CHAIN REMARK 500 4 ARG A 57 0.26 SIDE CHAIN REMARK 500 4 ARG A 87 0.29 SIDE CHAIN REMARK 500 4 ARG B 8 0.20 SIDE CHAIN REMARK 500 4 ARG B 41 0.32 SIDE CHAIN REMARK 500 4 ARG B 57 0.31 SIDE CHAIN REMARK 500 4 ARG B 87 0.10 SIDE CHAIN REMARK 500 5 ARG A 8 0.20 SIDE CHAIN REMARK 500 5 ARG A 41 0.10 SIDE CHAIN REMARK 500 5 ARG A 57 0.32 SIDE CHAIN REMARK 500 5 ARG A 87 0.19 SIDE CHAIN REMARK 500 5 ARG B 8 0.22 SIDE CHAIN REMARK 500 5 ARG B 41 0.12 SIDE CHAIN REMARK 500 5 ARG B 57 0.30 SIDE CHAIN REMARK 500 5 ARG B 87 0.29 SIDE CHAIN REMARK 500 6 ARG A 8 0.24 SIDE CHAIN REMARK 500 6 ARG A 41 0.16 SIDE CHAIN REMARK 500 6 ARG A 87 0.30 SIDE CHAIN REMARK 500 6 ARG B 8 0.20 SIDE CHAIN REMARK 500 6 ARG B 41 0.19 SIDE CHAIN REMARK 500 6 ARG B 57 0.31 SIDE CHAIN REMARK 500 6 ARG B 87 0.32 SIDE CHAIN REMARK 500 7 ARG A 8 0.26 SIDE CHAIN REMARK 500 7 ARG A 41 0.26 SIDE CHAIN REMARK 500 7 ARG A 57 0.15 SIDE CHAIN REMARK 500 7 ARG A 87 0.24 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 211 PLANE DEVIATIONS. 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 DMP B 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BVG RELATED DB: PDB REMARK 900 REPRESENTATIVE STRUCTURE DBREF 1BVE A 1 99 UNP P04585 POL_HV1H2 57 155 DBREF 1BVE B 1 99 UNP P04585 POL_HV1H2 57 155 SEQADV 1BVE ALA A 95 UNP P04585 CYS 151 ENGINEERED MUTATION SEQADV 1BVE ALA B 95 UNP P04585 CYS 151 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN VAL THR LEU TRP GLN ARG PRO LEU VAL THR ILE SEQRES 2 A 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL LEU GLU GLU MET SER LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE LEU ILE GLU SEQRES 6 A 99 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 99 GLN ILE GLY ALA THR LEU ASN PHE SEQRES 1 B 99 PRO GLN VAL THR LEU TRP GLN ARG PRO LEU VAL THR ILE SEQRES 2 B 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL LEU GLU GLU MET SER LEU PRO SEQRES 4 B 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE LEU ILE GLU SEQRES 6 B 99 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 B 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY ALA THR LEU ASN PHE HET DMP B 100 80 HETNAM DMP [4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6- HETNAM 2 DMP BIS(HYDROXY)-[1,3-BIS([4-HYDROXYMETHYL-PHENYL]METHYL)- HETNAM 3 DMP 4,7-BIS(PHEN YLMETHYL)]-2H-1,3-DIAZEPINONE HETSYN DMP DMP323(INHIBITOR OF DUPONT MERCK) FORMUL 3 DMP C35 H38 N2 O5 HELIX 1 1 ARG A 87 LEU A 90 1 4 HELIX 2 2 ARG B 87 LEU B 90 1 4 SHEET 1 A 3 LEU A 10 ILE A 13 0 SHEET 2 A 3 LYS A 20 LEU A 24 -1 N ALA A 22 O VAL A 11 SHEET 3 A 3 ASN A 83 ILE A 85 1 N ASN A 83 O LEU A 23 SHEET 1 B 2 THR A 31 LEU A 33 0 SHEET 2 B 2 VAL A 75 VAL A 77 1 N LEU A 76 O THR A 31 SHEET 1 C 2 TRP A 42 GLY A 48 0 SHEET 2 C 2 PHE A 53 TYR A 59 -1 N GLN A 58 O LYS A 43 SHEET 1 D 2 THR A 96 ASN A 98 0 SHEET 2 D 2 THR B 96 ASN B 98 -1 N ASN B 98 O THR A 96 SHEET 1 E 2 LEU B 10 ILE B 15 0 SHEET 2 E 2 GLN B 18 LEU B 23 -1 N ALA B 22 O VAL B 11 SHEET 1 F 3 VAL B 75 GLY B 78 0 SHEET 2 F 3 THR B 31 GLU B 34 1 N THR B 31 O LEU B 76 SHEET 3 F 3 ASN B 83 ILE B 85 -1 N ILE B 84 O VAL B 32 SHEET 1 G 2 LYS B 43 GLY B 48 0 SHEET 2 G 2 PHE B 53 GLN B 58 -1 N GLN B 58 O LYS B 43 SITE 1 AC1 17 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 2 AC1 17 GLY A 49 ILE A 50 PRO A 81 ILE A 84 SITE 3 AC1 17 ASP B 25 GLY B 27 ALA B 28 ASP B 29 SITE 4 AC1 17 ASP B 30 GLY B 49 ILE B 50 PRO B 81 SITE 5 AC1 17 ILE B 84 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1