HEADER HYDROLASE/HYDROLASE INHIBITOR 04-MAR-09 3GI0 TITLE CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED 203 AMINO ACID 'COVALENT TITLE 2 DIMER' [L-ALA51,D-ALA51'] HIV-1 PROTEASE MOLECULE COMPLEXED WITH JG- TITLE 3 365 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: COVALENT DIMER [L-ALA51,D-ALA51'] HIV-1 PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: JG-365 INHIBITOR; COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: TOTAL CHEMICAL PROTEIN SYNTHESIS; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 OTHER_DETAILS: CHEMICAL PEPTIDE SYNTHESIS KEYWDS BETA-BARREL, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.Y.TORBEEV,S.B.H.KENT REVDAT 4 15-NOV-23 3GI0 1 LINK ATOM REVDAT 3 06-SEP-23 3GI0 1 LINK REVDAT 2 07-JUN-17 3GI0 1 COMPND SOURCE REMARK REVDAT 1 10-AUG-11 3GI0 0 JRNL AUTH V.Y.TORBEEV,S.B.H.KENT JRNL TITL CORRELATIONS OF PROTEIN DYNAMICS WITH FUNCTION IN HIV-1 JRNL TITL 2 PROTEASE CATALYSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16579 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 883 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1206 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1810 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.2340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.65000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : 0.42000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.153 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.486 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1774 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2403 ; 1.673 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 228 ; 7.430 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 61 ;43.139 ;25.082 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 303 ;12.533 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;15.514 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 279 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1259 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 745 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1163 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 106 ; 0.174 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.044 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 52 ; 0.175 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.195 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1171 ; 1.057 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1839 ; 1.557 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 685 ; 2.569 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 564 ; 3.931 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. SEE REMARK 999 FOR THE SPECIAL STRUCTURAL SOLUTION REMARK 4 REMARK 4 3GI0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000051884. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR AND REMARK 200 K-B PAIR OF BIOMORPH MIRRORS FOR REMARK 200 VERTICAL AND HORIZONTAL FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17520 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP V.5 REMARK 200 STARTING MODEL: PDB ENTRY 3FSM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRATE, 0.2M SODIUM PHOPHATE,30% REMARK 280 (W/V) AMMONIUM SULFATE, 10% (V/V) DMSO , PH 6.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 25.58600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.47500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.22800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.47500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.58600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.22800 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SEE REMARK 999 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, D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 ILE B 50 O HOH A 263 1.88 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 PHE B 99 YCM B 100 -131.62 REMARK 500 JG3 C 5 ILE C 6 -110.06 REMARK 500 JG3 D 5 ILE D 6 -112.26 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 JG3 C 5 34.72 REMARK 500 JG3 D 5 33.37 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 DAL A 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAL B 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF JG-365 INHIBITOR REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF JG-365 INHIBITOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FSM RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 BOTH THE HIV-1 PROTEASE COVALENT DIMER [L-ALA51,D-ALA51'] (CHAINS A REMARK 999 AND B) AND JG-365 INHIBITOR (CHAINS C AND D) WERE CHEMICALLY REMARK 999 SYNTHESIZED WITH NON-NATURAL AMINO ACIDS INTRODUCED AT SEVERAL REMARK 999 POSITIONS. THE HIV-1 PROTEASE DIMER HAS TWO COVALENTLY LINKED REMARK 999 MONOMER PARTS, RESIDUES 1-99 AND RESIDUES 105-203, BOTH REMARK 999 REPRESENTING ANALOGUE OF HIV-1 PROTEASE CORRESPONDING TO THE REMARK 999 RESIDUES 491-589 OF UNP ENTRY P03369. THE REGION 1-99 OF THE FIRST REMARK 999 HALF AND 105-203 OF THE SECOND HALF SHARE THE SAME SEQUENCE EXCEPT REMARK 999 FOR THE 51ST RESIDUE, WHICH IS L-ALA(ALA51) IN REGION 1-99 AND D- REMARK 999 ALA (DAL155) IN REGION 105-203. THERE IS A SHORT LINKER REGION REMARK 999 (RESIDUES 100-104). THE TWO REGIONS (HALVES) ARE RELATED BY INTRA- REMARK 999 MOLECULAR PSEUDO-2-FOLD SYMMETRY, I.E. REGIONS 1-99 AND 105-203 REMARK 999 HAVE SIMILAR STRUCTURES BUT DO NOT SUPERIMPOSE COMPLETELY. MOREOVER, REMARK 999 THERE IS A DISORDER WITH RESPECT TO THE NON-CRYSTALLOGRAPHIC REMARK 999 PSEUDO-2-FOLD SYMMETRY AXIS OF THE COVELENT DIMER HIV-1 PROTEASE. REMARK 999 SUCH CONCLUSION IS BASED ON THE SPLIT OF THE DENSITY AT THE BETA- REMARK 999 TURN REGIONS FOR RESIDUES 49-52 AND 153-156, ALTHOUGH THE IS NO REMARK 999 DENSITY SPLIT BETWEEN TWO CONFORMERS FOR MOST OF THE ATOMS. TO REMARK 999 ACCOUNT FOR SUCH DISORDER, CHAINS A AND B, EACH REPRESENTING THE REMARK 999 SAME 203-AMINO ACID RESIDUE COVALENT DIMER HIV-1 PROTEASE WERE REMARK 999 INTRODUCED IN THE STRUCTURE SOLUTION. SO WERE CHAINS C AND D FOR REMARK 999 THE PEPTIDOMIMETIC JG-365 INHIBITOR, WHERE CHAIN C OF INHIBITOR REMARK 999 CORRESPONDS TO THE MODEL A OF THE COVELENT DIMER HIV-1 PROTEASE AND REMARK 999 CHAIN D CORRESPONDS TO MODEL B. THESE TWO MODELS, OR TWO REMARK 999 CONFORMATIONS OF ONE POLYMER CHAIN ARE RELATED TO EACH OTHER BY REMARK 999 PSEUDO-2-FOLD SYMMETRY. THE OCCUPANCIES WERE DETERMINED TO BE 0.65 REMARK 999 FOR CHAINS A AND C AND 0.35 FOR CHAINS B AND D, RESPECTIVELY. DBREF 3GI0 A 1 99 UNP P03369 POL_HV1A2 491 589 DBREF 3GI0 A 105 203 UNP P03369 POL_HV1A2 491 589 DBREF 3GI0 B 1 99 UNP P03369 POL_HV1A2 491 589 DBREF 3GI0 B 105 203 UNP P03369 POL_HV1A2 491 589 DBREF 3GI0 C 1 7 PDB 3GI0 3GI0 1 7 DBREF 3GI0 D 1 7 PDB 3GI0 3GI0 1 7 SEQADV 3GI0 LYS A 7 PDB POL_HV1A2 GLN 497 SEE REMARK 999 SEQADV 3GI0 ILE A 33 PDB POL_HV1A2 LEU 523 SEE REMARK 999 SEQADV 3GI0 NLE A 36 PDB POL_HV1A2 MET 526 SEE REMARK 999 SEQADV 3GI0 YCM A 41 PDB POL_HV1A2 LYS 531 SEE REMARK 999 SEQADV 3GI0 NLE A 46 PDB POL_HV1A2 MET 536 SEE REMARK 999 SEQADV 3GI0 ALA A 51 PDB POL_HV1A2 GLY 541 SEE REMARK 999 SEQADV 3GI0 ABA A 67 PDB POL_HV1A2 CYS 557 SEE REMARK 999 SEQADV 3GI0 ABA A 95 PDB POL_HV1A2 CYS 585 SEE REMARK 999 SEQADV 3GI0 YCM A 100 PDB POL_HV1A2 SEE REMARK 999 SEQADV 3GI0 GLY A 101 PDB POL_HV1A2 SEE REMARK 999 SEQADV 3GI0 GLY A 102 PDB POL_HV1A2 SEE REMARK 999 SEQADV 3GI0 GLY A 103 PDB POL_HV1A2 SEE REMARK 999 SEQADV 3GI0 GLY A 104 PDB POL_HV1A2 SEE REMARK 999 SEQADV 3GI0 LYS A 111 PDB POL_HV1A2 GLN 497 SEE REMARK 999 SEQADV 3GI0 ILE A 137 PDB POL_HV1A2 LEU 523 SEE REMARK 999 SEQADV 3GI0 NLE A 140 PDB POL_HV1A2 MET 526 SEE REMARK 999 SEQADV 3GI0 YCM A 145 PDB POL_HV1A2 LYS 531 SEE REMARK 999 SEQADV 3GI0 NLE A 150 PDB POL_HV1A2 MET 536 SEE REMARK 999 SEQADV 3GI0 DAL A 155 PDB POL_HV1A2 GLY 541 SEE REMARK 999 SEQADV 3GI0 ABA A 171 PDB POL_HV1A2 CYS 557 SEE REMARK 999 SEQADV 3GI0 ABA A 199 PDB POL_HV1A2 CYS 585 SEE REMARK 999 SEQADV 3GI0 LYS B 7 PDB POL_HV1A2 GLN 497 SEE REMARK 999 SEQADV 3GI0 ILE B 33 PDB POL_HV1A2 LEU 523 SEE REMARK 999 SEQADV 3GI0 NLE B 36 PDB POL_HV1A2 MET 526 SEE REMARK 999 SEQADV 3GI0 YCM B 41 PDB POL_HV1A2 LYS 531 SEE REMARK 999 SEQADV 3GI0 NLE B 46 PDB POL_HV1A2 MET 536 SEE REMARK 999 SEQADV 3GI0 ALA B 51 PDB POL_HV1A2 GLY 541 SEE REMARK 999 SEQADV 3GI0 ABA B 67 PDB POL_HV1A2 CYS 557 SEE REMARK 999 SEQADV 3GI0 ABA B 95 PDB POL_HV1A2 CYS 585 SEE REMARK 999 SEQADV 3GI0 YCM B 100 PDB POL_HV1A2 SEE REMARK 999 SEQADV 3GI0 GLY B 101 PDB POL_HV1A2 SEE REMARK 999 SEQADV 3GI0 GLY B 102 PDB POL_HV1A2 SEE REMARK 999 SEQADV 3GI0 GLY B 103 PDB POL_HV1A2 SEE REMARK 999 SEQADV 3GI0 GLY B 104 PDB POL_HV1A2 SEE REMARK 999 SEQADV 3GI0 LYS B 111 PDB POL_HV1A2 GLN 497 SEE REMARK 999 SEQADV 3GI0 ILE B 137 PDB POL_HV1A2 LEU 523 SEE REMARK 999 SEQADV 3GI0 NLE B 140 PDB POL_HV1A2 MET 526 SEE REMARK 999 SEQADV 3GI0 YCM B 145 PDB POL_HV1A2 LYS 531 SEE REMARK 999 SEQADV 3GI0 NLE B 150 PDB POL_HV1A2 MET 536 SEE REMARK 999 SEQADV 3GI0 DAL B 155 PDB POL_HV1A2 GLY 541 SEE REMARK 999 SEQADV 3GI0 ABA B 171 PDB POL_HV1A2 CYS 557 SEE REMARK 999 SEQADV 3GI0 ABA B 199 PDB POL_HV1A2 CYS 585 SEE REMARK 999 SEQRES 1 A 203 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 203 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 203 GLY ALA ASP ASP THR VAL ILE GLU GLU NLE ASN LEU PRO SEQRES 4 A 203 GLY YCM TRP LYS PRO LYS NLE ILE GLY GLY ILE ALA GLY SEQRES 5 A 203 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL GLU SEQRES 6 A 203 ILE ABA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 203 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 203 GLN ILE GLY ABA THR LEU ASN PHE YCM GLY GLY GLY GLY SEQRES 9 A 203 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 10 A 203 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 11 A 203 GLY ALA ASP ASP THR VAL ILE GLU GLU NLE ASN LEU PRO SEQRES 12 A 203 GLY YCM TRP LYS PRO LYS NLE ILE GLY GLY ILE DAL GLY SEQRES 13 A 203 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL GLU SEQRES 14 A 203 ILE ABA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 15 A 203 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 16 A 203 GLN ILE GLY ABA THR LEU ASN PHE SEQRES 1 B 203 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 B 203 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 B 203 GLY ALA ASP ASP THR VAL ILE GLU GLU NLE ASN LEU PRO SEQRES 4 B 203 GLY YCM TRP LYS PRO LYS NLE ILE GLY GLY ILE ALA GLY SEQRES 5 B 203 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL GLU SEQRES 6 B 203 ILE ABA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 B 203 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 203 GLN ILE GLY ABA THR LEU ASN PHE YCM GLY GLY GLY GLY SEQRES 9 B 203 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 10 B 203 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 11 B 203 GLY ALA ASP ASP THR VAL ILE GLU GLU NLE ASN LEU PRO SEQRES 12 B 203 GLY YCM TRP LYS PRO LYS NLE ILE GLY GLY ILE DAL GLY SEQRES 13 B 203 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL GLU SEQRES 14 B 203 ILE ABA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 15 B 203 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 16 B 203 GLN ILE GLY ABA THR LEU ASN PHE SEQRES 1 C 7 ACE SER LEU ASN JG3 ILE VME SEQRES 1 D 7 ACE SER LEU ASN JG3 ILE VME MODRES 3GI0 NLE A 36 LEU NORLEUCINE MODRES 3GI0 YCM A 41 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 3GI0 NLE A 46 LEU NORLEUCINE MODRES 3GI0 ABA A 67 ALA ALPHA-AMINOBUTYRIC ACID MODRES 3GI0 ABA A 95 ALA ALPHA-AMINOBUTYRIC ACID MODRES 3GI0 YCM A 100 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 3GI0 NLE A 140 LEU NORLEUCINE MODRES 3GI0 YCM A 145 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 3GI0 NLE A 150 LEU NORLEUCINE MODRES 3GI0 ABA A 171 ALA ALPHA-AMINOBUTYRIC ACID MODRES 3GI0 ABA A 199 ALA ALPHA-AMINOBUTYRIC ACID MODRES 3GI0 NLE B 36 LEU NORLEUCINE MODRES 3GI0 YCM B 41 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 3GI0 NLE B 46 LEU NORLEUCINE MODRES 3GI0 ABA B 67 ALA ALPHA-AMINOBUTYRIC ACID MODRES 3GI0 ABA B 95 ALA ALPHA-AMINOBUTYRIC ACID MODRES 3GI0 YCM B 100 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 3GI0 NLE B 140 LEU NORLEUCINE MODRES 3GI0 YCM B 145 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 3GI0 NLE B 150 LEU NORLEUCINE MODRES 3GI0 ABA B 171 ALA ALPHA-AMINOBUTYRIC ACID MODRES 3GI0 ABA B 199 ALA ALPHA-AMINOBUTYRIC ACID HET NLE A 36 8 HET YCM A 41 10 HET NLE A 46 8 HET ABA A 67 6 HET ABA A 95 6 HET YCM A 100 10 HET NLE A 140 8 HET YCM A 145 10 HET NLE A 150 8 HET DAL A 155 5 HET ABA A 171 6 HET ABA A 199 6 HET NLE B 36 8 HET YCM B 41 10 HET NLE B 46 8 HET ABA B 67 6 HET ABA B 95 6 HET YCM B 100 10 HET NLE B 140 8 HET YCM B 145 10 HET NLE B 150 8 HET DAL B 155 5 HET ABA B 171 6 HET ABA B 199 6 HET ACE C 1 3 HET JG3 C 5 19 HET VME C 7 9 HET ACE D 1 3 HET JG3 D 5 19 HET VME D 7 9 HETNAM NLE NORLEUCINE HETNAM YCM S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HETNAM ABA ALPHA-AMINOBUTYRIC ACID HETNAM DAL D-ALANINE HETNAM ACE ACETYL GROUP HETNAM JG3 1-[(2S,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]-L-PROLINE HETNAM VME METHYL L-VALINATE HETSYN YCM CYSTEINE-S-ACETAMIDE HETSYN VME O-METHYLVALINE FORMUL 1 NLE 8(C6 H13 N O2) FORMUL 1 YCM 6(C5 H10 N2 O3 S) FORMUL 1 ABA 8(C4 H9 N O2) FORMUL 1 DAL 2(C3 H7 N O2) FORMUL 3 ACE 2(C2 H4 O) FORMUL 3 JG3 2(C15 H22 N2 O3) FORMUL 3 VME 2(C6 H13 N O2) FORMUL 5 HOH *96(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 YCM A 100 GLY A 103 5 4 HELIX 3 3 GLY A 190 THR A 195 1 6 SHEET 1 A 4 GLN A 2 ILE A 3 0 SHEET 2 A 4 THR A 200 ASN A 202 -1 O LEU A 201 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR A 200 SHEET 4 A 4 GLN A 106 ILE A 107 -1 O ILE A 107 N LEU A 97 SHEET 1 B 8 TRP A 42 GLY A 49 0 SHEET 2 B 8 GLY A 52 ILE A 66 -1 O VAL A 56 N LYS A 45 SHEET 3 B 8 HIS A 69 VAL A 77 -1 O HIS A 69 N ILE A 66 SHEET 4 B 8 VAL A 32 ILE A 33 1 N ILE A 33 O LEU A 76 SHEET 5 B 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 B 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 B 8 LEU A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 B 8 GLY A 52 ILE A 66 -1 O GLU A 65 N ARG A 14 SHEET 1 C 8 LYS A 147 GLY A 153 0 SHEET 2 C 8 GLY A 156 ILE A 170 -1 O VAL A 160 N LYS A 149 SHEET 3 C 8 HIS A 173 VAL A 181 -1 O HIS A 173 N ILE A 170 SHEET 4 C 8 VAL A 136 ILE A 137 1 N ILE A 137 O LEU A 180 SHEET 5 C 8 ILE A 188 ILE A 189 -1 O ILE A 188 N VAL A 136 SHEET 6 C 8 GLN A 122 LEU A 128 1 N LEU A 127 O ILE A 189 SHEET 7 C 8 LEU A 114 ILE A 119 -1 N ILE A 119 O GLN A 122 SHEET 8 C 8 GLY A 156 ILE A 170 -1 O GLU A 169 N ARG A 118 LINK C AGLU A 35 N ANLE A 36 1555 1555 1.32 LINK C ANLE A 36 N AASN A 37 1555 1555 1.33 LINK C AGLY A 40 N AYCM A 41 1555 1555 1.33 LINK C AYCM A 41 N ATRP A 42 1555 1555 1.34 LINK C ALYS A 45 N ANLE A 46 1555 1555 1.34 LINK C ANLE A 46 N AILE A 47 1555 1555 1.33 LINK C AILE A 66 N AABA A 67 1555 1555 1.33 LINK C AABA A 67 N AGLY A 68 1555 1555 1.33 LINK C AGLY A 94 N AABA A 95 1555 1555 1.33 LINK C AABA A 95 N ATHR A 96 1555 1555 1.34 LINK C APHE A 99 N AYCM A 100 1555 1555 1.33 LINK C AYCM A 100 N AGLY A 101 1555 1555 1.33 LINK C AGLU A 139 N ANLE A 140 1555 1555 1.33 LINK C ANLE A 140 N AASN A 141 1555 1555 1.32 LINK C AGLY A 144 N AYCM A 145 1555 1555 1.34 LINK C AYCM A 145 N ATRP A 146 1555 1555 1.33 LINK C ALYS A 149 N ANLE A 150 1555 1555 1.33 LINK C ANLE A 150 N AILE A 151 1555 1555 1.33 LINK C AILE A 154 N ADAL A 155 1555 1555 1.34 LINK C ADAL A 155 N AGLY A 156 1555 1555 1.33 LINK C AILE A 170 N AABA A 171 1555 1555 1.34 LINK C AABA A 171 N AGLY A 172 1555 1555 1.34 LINK C AGLY A 198 N AABA A 199 1555 1555 1.33 LINK C AABA A 199 N ATHR A 200 1555 1555 1.33 LINK C BGLU B 35 N BNLE B 36 1555 1555 1.33 LINK C BNLE B 36 N BASN B 37 1555 1555 1.32 LINK C BGLY B 40 N BYCM B 41 1555 1555 1.34 LINK C BYCM B 41 N BTRP B 42 1555 1555 1.33 LINK C BLYS B 45 N BNLE B 46 1555 1555 1.33 LINK C BNLE B 46 N BILE B 47 1555 1555 1.33 LINK C BILE B 66 N BABA B 67 1555 1555 1.34 LINK C BABA B 67 N BGLY B 68 1555 1555 1.34 LINK C BGLY B 94 N BABA B 95 1555 1555 1.33 LINK C BABA B 95 N BTHR B 96 1555 1555 1.33 LINK C BPHE B 99 N BYCM B 100 1555 1555 1.32 LINK C BYCM B 100 N BGLY B 101 1555 1555 1.33 LINK C BGLU B 139 N BNLE B 140 1555 1555 1.32 LINK C BNLE B 140 N BASN B 141 1555 1555 1.33 LINK C BGLY B 144 N BYCM B 145 1555 1555 1.33 LINK C BYCM B 145 N BTRP B 146 1555 1555 1.34 LINK C BLYS B 149 N BNLE B 150 1555 1555 1.34 LINK C BNLE B 150 N BILE B 151 1555 1555 1.33 LINK C BILE B 154 N BDAL B 155 1555 1555 1.32 LINK C BDAL B 155 N BGLY B 156 1555 1555 1.33 LINK C BILE B 170 N BABA B 171 1555 1555 1.33 LINK C BABA B 171 N BGLY B 172 1555 1555 1.33 LINK C BGLY B 198 N BABA B 199 1555 1555 1.33 LINK C BABA B 199 N BTHR B 200 1555 1555 1.34 LINK C AACE C 1 N ASER C 2 1555 1555 1.34 LINK C AASN C 4 N AJG3 C 5 1555 1555 1.33 LINK C AJG3 C 5 N AILE C 6 1555 1555 1.33 LINK C AILE C 6 N AVME C 7 1555 1555 1.32 LINK C BACE D 1 N BSER D 2 1555 1555 1.33 LINK C BASN D 4 N BJG3 D 5 1555 1555 1.33 LINK C BJG3 D 5 N BILE D 6 1555 1555 1.33 LINK C BILE D 6 N BVME D 7 1555 1555 1.33 SITE 1 AC1 7 ALA A 51 PHE A 53 ILE A 54 GLY A 153 SITE 2 AC1 7 ILE A 154 GLY A 156 HOH A 263 SITE 1 AC2 7 HOH A 259 ALA B 51 GLY B 52 PHE B 53 SITE 2 AC2 7 GLY B 153 ILE B 154 GLY B 156 SITE 1 AC3 20 ARG A 8 ASP A 25 GLY A 27 ALA A 28 SITE 2 AC3 20 ASP A 29 ASP A 30 ILE A 47 GLY A 48 SITE 3 AC3 20 GLY A 49 ILE A 50 ARG A 112 ASP A 129 SITE 4 AC3 20 GLY A 131 ALA A 132 ASP A 133 GLY A 152 SITE 5 AC3 20 GLY A 153 PRO A 185 VAL A 186 HOH A 207 SITE 1 AC4 20 HOH A 207 ARG B 8 ASP B 25 GLY B 27 SITE 2 AC4 20 ALA B 28 ASP B 29 ASP B 30 ILE B 47 SITE 3 AC4 20 GLY B 48 GLY B 49 ILE B 50 ILE B 84 SITE 4 AC4 20 ASP B 129 GLY B 131 ASP B 133 GLY B 152 SITE 5 AC4 20 GLY B 153 ILE B 154 PRO B 185 ILE B 188 CRYST1 51.172 58.456 60.950 90.00 90.00 90.00 P 21 21 21 8 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 0.019542 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016407 0.00000