HEADER HYDROLASE/HYDROLASE INHIBITOR 11-NOV-06 2J9J TITLE ATOMIC-RESOLUTION CRYSTAL STRUCTURE OF CHEMICALLY-SYNTHESIZED HIV-1 TITLE 2 PROTEASE COMPLEXED WITH INHIBITOR JG-365 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIV1-PROTEASE; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEASE; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: HIV1-PROTEASE; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: INHIBITOR MOLECULE JG365; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 6 ORGANISM_TAXID: 11676; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX, PROTEASE, HYDROLASE, HIGH KEYWDS 2 RESOLUTION, RNA-DIRECTED DNA POLYMERASE, ASPARTYL PROTEASE, HUMAN KEYWDS 3 IMMUNODEFICIENCY VIRUS 1, HYDROLASE- HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION NUMMDL 2 AUTHOR E.MALITO,Y.SHEN,E.C.B.JOHNSON,W.J.TANG REVDAT 10 13-DEC-23 2J9J 1 REMARK REVDAT 9 15-NOV-23 2J9J 1 REMARK ATOM REVDAT 8 22-MAY-19 2J9J 1 REMARK LINK REVDAT 7 18-OCT-17 2J9J 1 REMARK REVDAT 6 15-FEB-17 2J9J 1 SOURCE REVDAT 5 20-JUL-11 2J9J 1 SOURCE KEYWDS REVDAT REMARK REVDAT 5 2 1 MASTER REVDAT 4 13-JUL-11 2J9J 1 VERSN REVDAT 3 24-FEB-09 2J9J 1 VERSN REVDAT 2 16-OCT-07 2J9J 1 JRNL REVDAT 1 28-AUG-07 2J9J 0 JRNL AUTH E.C.B.JOHNSON,E.MALITO,Y.SHEN,B.PENTELUTE,D.RICH,J.FLORIAN, JRNL AUTH 2 W.J.TANG,S.B.H.KENT JRNL TITL INSIGHTS FROM ATOMIC-RESOLUTION X-RAY STRUCTURES OF JRNL TITL 2 CHEMICALLY SYNTHESIZED HIV-1 PROTEASE IN COMPLEX WITH JRNL TITL 3 INHIBITORS. JRNL REF J.MOL.BIOL. V. 373 573 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17869270 JRNL DOI 10.1016/J.JMB.2007.07.054 REMARK 2 REMARK 2 RESOLUTION. 1.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.131 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.142 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 11.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 8237 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 73981 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.120 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.130 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 11.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 6760 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 60671 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1570 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 240 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1950.7 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1665.2 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 32 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 18720 REMARK 3 NUMBER OF RESTRAINTS : 23809 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 ANGLE DISTANCES (A) : 0.041 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.034 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.120 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.103 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.065 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.043 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.108 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2J9J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1290030396. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 150; NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 14-BM-C; 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL; NULL REMARK 200 DETECTOR MANUFACTURER : NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82488 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.040 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 7HVP REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 25.27400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.44450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.40700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.44450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.27400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.40700 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE JG-365 IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: JG-365 REMARK 400 CHAIN: C REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 1 ACE C 0 REMARK 465 2 ACE C 0 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 1 ASN B 37 CG OD1 ND2 REMARK 470 2 ASN B 37 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 ILE A 50 C GLY A 51 N 0.300 REMARK 500 1 ILE A 50 C GLY A 51 N -0.985 REMARK 500 1 ILE B 50 C GLY B 51 N -0.628 REMARK 500 1 PHE B 99 C PHE B 99 OXT 0.116 REMARK 500 2 ILE A 50 C GLY A 51 N 0.300 REMARK 500 2 ILE A 50 C GLY A 51 N -0.985 REMARK 500 2 ILE B 50 C GLY B 51 N -0.628 REMARK 500 2 PHE B 99 C PHE B 99 OXT 0.116 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 1 ARG A 14 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 ASP A 30 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 GLU A 35 CB - CG - CD ANGL. DEV. = 22.5 DEGREES REMARK 500 1 GLY A 49 O - C - N ANGL. DEV. = 10.8 DEGREES REMARK 500 1 ILE A 50 CA - C - N ANGL. DEV. = 50.7 DEGREES REMARK 500 1 ILE A 50 CA - C - N ANGL. DEV. = 40.4 DEGREES REMARK 500 1 ILE A 50 O - C - N ANGL. DEV. = -53.7 DEGREES REMARK 500 1 ILE A 50 O - C - N ANGL. DEV. = -79.6 DEGREES REMARK 500 1 GLY A 51 C - N - CA ANGL. DEV. = 27.9 DEGREES REMARK 500 1 PHE A 53 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 PHE A 53 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 ASP A 60 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 ARG B 14 CD - NE - CZ ANGL. DEV. = 24.8 DEGREES REMARK 500 1 ARG B 14 NE - CZ - NH2 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 ILE B 50 CA - C - N ANGL. DEV. = 47.9 DEGREES REMARK 500 1 ILE B 50 CA - C - N ANGL. DEV. = 57.4 DEGREES REMARK 500 1 ILE B 50 O - C - N ANGL. DEV. = -52.3 DEGREES REMARK 500 1 ILE B 50 O - C - N ANGL. DEV. = -53.2 DEGREES REMARK 500 1 GLY B 51 C - N - CA ANGL. DEV. = 30.4 DEGREES REMARK 500 1 GLY B 51 C - N - CA ANGL. DEV. = 38.7 DEGREES REMARK 500 1 ARG B 57 CD - NE - CZ ANGL. DEV. = 12.5 DEGREES REMARK 500 1 ARG B 57 NH1 - CZ - NH2 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 ARG B 57 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 ASP B 60 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 VAL B 82 CG1 - CB - CG2 ANGL. DEV. = -10.1 DEGREES REMARK 500 2 ARG A 14 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 ASP A 30 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 GLU A 35 CB - CG - CD ANGL. DEV. = 22.5 DEGREES REMARK 500 2 GLY A 49 O - C - N ANGL. DEV. = 10.8 DEGREES REMARK 500 2 ILE A 50 CA - C - N ANGL. DEV. = 50.7 DEGREES REMARK 500 2 ILE A 50 CA - C - N ANGL. DEV. = 40.4 DEGREES REMARK 500 2 ILE A 50 O - C - N ANGL. DEV. = -53.7 DEGREES REMARK 500 2 ILE A 50 O - C - N ANGL. DEV. = -79.6 DEGREES REMARK 500 2 GLY A 51 C - N - CA ANGL. DEV. = 27.9 DEGREES REMARK 500 2 PHE A 53 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 PHE A 53 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 ASP A 60 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 2 ARG B 14 CD - NE - CZ ANGL. DEV. = 24.8 DEGREES REMARK 500 2 ARG B 14 NE - CZ - NH2 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 ILE B 50 CA - C - N ANGL. DEV. = 47.9 DEGREES REMARK 500 2 ILE B 50 CA - C - N ANGL. DEV. = 57.4 DEGREES REMARK 500 2 ILE B 50 O - C - N ANGL. DEV. = -52.3 DEGREES REMARK 500 2 ILE B 50 O - C - N ANGL. DEV. = -53.2 DEGREES REMARK 500 2 GLY B 51 C - N - CA ANGL. DEV. = 30.4 DEGREES REMARK 500 2 GLY B 51 C - N - CA ANGL. DEV. = 38.7 DEGREES REMARK 500 2 ARG B 57 CD - NE - CZ ANGL. DEV. = 12.5 DEGREES REMARK 500 2 ARG B 57 NH1 - CZ - NH2 ANGL. DEV. = 7.6 DEGREES REMARK 500 2 ARG B 57 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 ASP B 60 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 2 VAL B 82 CG1 - CB - CG2 ANGL. DEV. = -10.1 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 1 ILE A 50 5.61 -58.71 REMARK 500 1 ILE B 50 89.71 -63.99 REMARK 500 2 ILE A 50 5.61 -58.71 REMARK 500 2 ILE B 50 89.71 -63.99 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 ILE A 50 GLY A 51 1 -71.45 REMARK 500 ILE B 50 GLY B 51 1 70.88 REMARK 500 JG3 C 4 ILE C 5 1 -108.57 REMARK 500 ILE A 50 GLY A 51 2 -71.45 REMARK 500 ILE B 50 GLY B 51 2 70.88 REMARK 500 JG3 C 4 ILE C 5 2 -110.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 ILE A 50 -38.20 REMARK 500 1 ILE A 50 -145.76 REMARK 500 1 ILE B 50 42.35 REMARK 500 1 ILE B 50 -20.59 REMARK 500 1 JG3 C 4 33.59 REMARK 500 2 ILE A 50 -38.20 REMARK 500 2 ILE A 50 -145.76 REMARK 500 2 ILE B 50 42.35 REMARK 500 2 ILE B 50 -20.59 REMARK 500 2 JG3 C 4 33.36 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 A2097 DISTANCE = 14.03 ANGSTROMS REMARK 525 HOH B2032 DISTANCE = 13.66 ANGSTROMS REMARK 525 HOH B2047 DISTANCE = 11.84 ANGSTROMS REMARK 525 HOH B2084 DISTANCE = 15.99 ANGSTROMS REMARK 525 HOH B2100 DISTANCE = 19.62 ANGSTROMS REMARK 525 HOH B2114 DISTANCE = 13.94 ANGSTROMS REMARK 525 HOH A2097 DISTANCE = 14.03 ANGSTROMS REMARK 525 HOH B2032 DISTANCE = 13.66 ANGSTROMS REMARK 525 HOH B2047 DISTANCE = 11.84 ANGSTROMS REMARK 525 HOH B2084 DISTANCE = 15.99 ANGSTROMS REMARK 525 HOH B2100 DISTANCE = 19.62 ANGSTROMS REMARK 525 HOH B2114 DISTANCE = 13.94 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF INHIBITOR MOLECULE REMARK 800 JG365 DBREF 2J9J A 1 99 UNP O38907 O38907_9HIV1 1 99 DBREF 2J9J B 1 99 UNP O38907 O38907_9HIV1 1 99 DBREF 2J9J C 0 6 PDB 2J9J 2J9J 0 6 SEQADV 2J9J LYS A 7 UNP O38907 GLN 7 CONFLICT SEQADV 2J9J NLE A 36 UNP O38907 MET 36 CONFLICT SEQADV 2J9J SLZ A 41 UNP O38907 ARG 41 CONFLICT SEQADV 2J9J NLE A 46 UNP O38907 MET 46 CONFLICT SEQADV 2J9J ILE A 62 UNP O38907 VAL 62 CONFLICT SEQADV 2J9J VAL A 64 UNP O38907 ILE 64 CONFLICT SEQADV 2J9J ILE A 93 UNP O38907 LEU 93 CONFLICT SEQADV 2J9J LYS B 7 UNP O38907 GLN 7 CONFLICT SEQADV 2J9J ASN B 18 UNP O38907 GLN 18 CONFLICT SEQADV 2J9J NLE B 36 UNP O38907 MET 36 CONFLICT SEQADV 2J9J SLZ B 41 UNP O38907 ARG 41 CONFLICT SEQADV 2J9J NLE B 46 UNP O38907 MET 46 CONFLICT SEQADV 2J9J ILE B 62 UNP O38907 VAL 62 CONFLICT SEQADV 2J9J VAL B 64 UNP O38907 ILE 64 CONFLICT SEQADV 2J9J ILE B 93 UNP O38907 LEU 93 CONFLICT SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 99 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL ILE GLU GLU NLE ASN LEU PRO SEQRES 4 A 99 GLY SLZ TRP LYS PRO LYS NLE ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL GLU SEQRES 6 A 99 ILE ABA 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 ABA THR LEU ASN PHE SEQRES 1 B 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 B 99 ARG ILE GLY GLY ASN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL ILE GLU GLU NLE ASN LEU PRO SEQRES 4 B 99 GLY SLZ TRP LYS PRO LYS NLE ILE GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL GLU SEQRES 6 B 99 ILE ABA 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 ABA THR LEU ASN PHE SEQRES 1 C 7 ACE SER LEU ASN JG3 ILE VME MODRES 2J9J NLE A 36 LEU NORLEUCINE MODRES 2J9J SLZ A 41 LYS L-THIALYSINE MODRES 2J9J NLE A 46 LEU NORLEUCINE MODRES 2J9J ABA A 67 ALA ALPHA-AMINOBUTYRIC ACID MODRES 2J9J ABA A 95 ALA ALPHA-AMINOBUTYRIC ACID MODRES 2J9J NLE B 36 LEU NORLEUCINE MODRES 2J9J SLZ B 41 LYS L-THIALYSINE MODRES 2J9J NLE B 46 LEU NORLEUCINE MODRES 2J9J ABA B 67 ALA ALPHA-AMINOBUTYRIC ACID MODRES 2J9J ABA B 95 ALA ALPHA-AMINOBUTYRIC ACID HET NLE A 36 8 HET SLZ A 41 9 HET NLE A 46 8 HET ABA A 67 9 HET ABA A 95 6 HET NLE B 36 8 HET SLZ B 41 9 HET NLE B 46 8 HET ABA B 67 6 HET ABA B 95 6 HET JG3 C 4 19 HET VME C 6 9 HET SO4 A1105 5 HET SO4 A1106 5 HET GOL A1107 6 HET GOL A1108 6 HET SO4 B1105 5 HET ACT B1106 4 HETNAM NLE NORLEUCINE HETNAM SLZ L-THIALYSINE HETNAM ABA ALPHA-AMINOBUTYRIC ACID HETNAM JG3 1-[(2S,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]-L-PROLINE HETNAM VME METHYL L-VALINATE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN VME O-METHYLVALINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 NLE 4(C6 H13 N O2) FORMUL 1 SLZ 2(C5 H12 N2 O2 S) FORMUL 1 ABA 4(C4 H9 N O2) FORMUL 3 JG3 C15 H22 N2 O3 FORMUL 3 VME C6 H13 N O2 FORMUL 4 SO4 3(O4 S 2-) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 9 ACT C2 H3 O2 1- FORMUL 10 HOH *240(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 THR B 91 1 6 HELIX 3 3 GLN B 92 GLY B 94 5 3 SHEET 1 AA 2 GLN A 2 ILE A 3 0 SHEET 2 AA 2 LEU B 97 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 1 AB 8 LEU A 10 ILE A 15 0 SHEET 2 AB 8 GLN A 18 LEU A 24 -1 O GLN A 18 N ILE A 15 SHEET 3 AB 8 ILE A 84 ILE A 85 1 N ILE A 85 O LEU A 23 SHEET 4 AB 8 VAL A 32 ILE A 33 -1 O VAL A 32 N ILE A 84 SHEET 5 AB 8 LYS A 70 VAL A 77 1 O LEU A 76 N ILE A 33 SHEET 6 AB 8 GLY A 52 GLU A 65 -1 O ARG A 57 N VAL A 77 SHEET 7 AB 8 LEU A 10 ILE A 15 -1 O ARG A 14 N GLU A 65 SHEET 8 AB 8 LEU A 10 ILE A 15 0 SHEET 1 AC 2 LEU A 97 ASN A 98 0 SHEET 2 AC 2 GLN B 2 ILE B 3 -1 O ILE B 3 N LEU A 97 SHEET 1 BA 8 LEU B 10 ILE B 15 0 SHEET 2 BA 8 ASN B 18 LEU B 24 -1 O ASN B 18 N ILE B 15 SHEET 3 BA 8 ILE B 84 ILE B 85 1 N ILE B 85 O LEU B 23 SHEET 4 BA 8 VAL B 32 ILE B 33 -1 O VAL B 32 N ILE B 84 SHEET 5 BA 8 LYS B 70 VAL B 77 1 O LEU B 76 N ILE B 33 SHEET 6 BA 8 GLY B 52 GLU B 65 -1 O ARG B 57 N VAL B 77 SHEET 7 BA 8 LEU B 10 ILE B 15 -1 O ARG B 14 N GLU B 65 SHEET 8 BA 8 LEU B 10 ILE B 15 0 LINK C AGLU A 35 N ANLE A 36 1555 1555 1.33 LINK C ANLE A 36 N AASN A 37 1555 1555 1.32 LINK C AGLY A 40 N ASLZ A 41 1555 1555 1.33 LINK C ASLZ A 41 N ATRP A 42 1555 1555 1.31 LINK C ALYS A 45 N ANLE A 46 1555 1555 1.32 LINK C ANLE A 46 N AILE A 47 1555 1555 1.32 LINK C AILE A 66 N AABA A 67 1555 1555 1.33 LINK C AABA A 67 N AGLY A 68 1555 1555 1.34 LINK C AGLY A 94 N AABA A 95 1555 1555 1.31 LINK C AABA A 95 N ATHR A 96 1555 1555 1.33 LINK C AGLU B 35 N ANLE B 36 1555 1555 1.31 LINK C ANLE B 36 N AASN B 37 1555 1555 1.36 LINK C AGLY B 40 N ASLZ B 41 1555 1555 1.33 LINK C ASLZ B 41 N ATRP B 42 1555 1555 1.31 LINK C ALYS B 45 N ANLE B 46 1555 1555 1.33 LINK C ANLE B 46 N AILE B 47 1555 1555 1.31 LINK C AILE B 66 N AABA B 67 1555 1555 1.36 LINK C AABA B 67 N AGLY B 68 1555 1555 1.33 LINK C AGLY B 94 N AABA B 95 1555 1555 1.34 LINK C AABA B 95 N ATHR B 96 1555 1555 1.34 LINK C AASN C 3 N AJG3 C 4 1555 1555 1.32 LINK C AJG3 C 4 N AILE C 5 1555 1555 1.35 CISPEP 1 ILE B 50 GLY B 51 1 -26.13 CISPEP 2 ILE B 50 GLY B 51 2 -26.13 SITE 1 AC1 6 PRO A 1 ASN A 37 ARG A 57 HIS A 69 SITE 2 AC1 6 HOH A2119 HOH B2102 SITE 1 AC2 8 ARG A 14 HOH A2033 HOH A2120 HOH A2121 SITE 2 AC2 8 HOH A2122 ARG B 14 GLY B 17 PRO B 63 SITE 1 AC3 7 PHE A 99 HOH A2088 HOH A2123 NLE B 46 SITE 2 AC3 7 PHE B 53 LYS B 55 HIS B 69 SITE 1 AC4 6 THR A 12 SLZ A 41 TRP A 42 ABA A 67 SITE 2 AC4 6 HOH A2124 HOH A2125 SITE 1 AC5 7 GLY A 68 HIS A 69 LYS A 70 HOH A2088 SITE 2 AC5 7 PRO B 1 LYS B 55 HOH B2109 SITE 1 AC6 6 LYS A 55 LYS A 70 ARG B 14 LYS B 70 SITE 2 AC6 6 HOH B2110 HOH B2112 SITE 1 AC7 24 ARG A 8 ASP A 25 GLY A 27 ALA A 28 SITE 2 AC7 24 ASP A 29 ASP A 30 LYS A 45 ILE A 47 SITE 3 AC7 24 GLY A 48 GLY A 49 ILE A 50 ILE A 84 SITE 4 AC7 24 HOH A2046 HOH A2064 ASP B 25 GLY B 27 SITE 5 AC7 24 ALA B 28 ASP B 29 GLY B 48 GLY B 49 SITE 6 AC7 24 VAL B 82 ILE B 84 HOH B2066 HOH B2106 CRYST1 50.548 58.814 60.889 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 0.019783 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017003 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016423 0.00000 MODEL 1