HEADER HYDROLASE/HYDROLASE INHIBITOR 10-JAN-09 3FSM TITLE CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED 203 AMINO ACID 'COVALENT TITLE 2 DIMER' [L-ALA51,D-ALA51'] HIV-1 PROTEASE MOLECULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COVALENT DIMER [L-ALA51, D-ALA51'] HIV-1 PROTEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: TOTAL CHEMICAL PROTEIN SYNTHESIS KEYWDS ASYMMETRIC DIMER, COVALENT DIMER, BETA-SHEET, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.Y.TORBEEV,S.B.H.KENT REVDAT 9 13-MAR-24 3FSM 1 COMPND SOURCE REVDAT 8 22-NOV-23 3FSM 1 REMARK REVDAT 7 06-SEP-23 3FSM 1 REMARK SHEET LINK REVDAT 6 01-NOV-17 3FSM 1 REMARK REVDAT 5 11-JAN-12 3FSM 1 JRNL REVDAT 4 13-JUL-11 3FSM 1 VERSN REVDAT 3 19-MAY-10 3FSM 1 HEADER REVDAT 2 19-JAN-10 3FSM 1 HET HETATM REVDAT 1 05-JAN-10 3FSM 0 JRNL AUTH V.Y.TORBEEV,H.RAGHURAMAN,D.HAMELBERG,M.TONELLI,W.M.WESTLER, JRNL AUTH 2 E.PEROZO,S.B.KENT JRNL TITL PROTEIN CONFORMATIONAL DYNAMICS IN THE MECHANISM OF HIV-1 JRNL TITL 2 PROTEASE CATALYSIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 20982 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 22158985 JRNL DOI 10.1073/PNAS.1111202108 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 25039 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1274 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1654 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1545 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 118 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) : 25.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : -0.32000 REMARK 3 B33 (A**2) : 0.26000 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): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.804 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1629 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1098 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2203 ; 1.634 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2705 ; 0.901 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 204 ; 6.412 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 59 ;42.541 ;24.915 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 288 ;12.681 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;15.876 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 259 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1750 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 280 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 217 ; 0.192 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1051 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 767 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 874 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 56 ; 0.131 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.010 ; 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): 5 ; 0.115 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 35 ; 0.177 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.158 ; 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): 1062 ; 1.081 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 431 ; 0.320 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1674 ; 1.617 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 638 ; 2.449 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 529 ; 3.694 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 203 REMARK 3 ORIGIN FOR THE GROUP (A): 5.0890 1.1810 18.2140 REMARK 3 T TENSOR REMARK 3 T11: -0.1160 T22: -0.1238 REMARK 3 T33: -0.1663 T12: -0.0017 REMARK 3 T13: -0.0033 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 2.3501 L22: 2.0535 REMARK 3 L33: 1.3060 L12: -0.8509 REMARK 3 L13: 0.4832 L23: 0.6234 REMARK 3 S TENSOR REMARK 3 S11: 0.0241 S12: 0.0982 S13: -0.0555 REMARK 3 S21: 0.0313 S22: 0.0558 S23: -0.0424 REMARK 3 S31: 0.0350 S32: 0.1324 S33: -0.0799 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 3FSM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000050991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-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-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03320 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 WITH TWO ADDITIONAL HORIZONTALLY REMARK 200 DEFLECTING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25109 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 81.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6360 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.67700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2O40 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRATE, 0.2M SODIUM PHOPHATE, REMARK 280 30% (W/V) AMMONIUM SULFATE, 10% (V/V) DMSO , PH 6.0, VAPOR REMARK 280 DIFFUSION, 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 25.73600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.72500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.14300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.72500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.73600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.14300 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: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: 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 ASP A 25 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 191 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 39 105.22 -54.35 REMARK 500 ABA A 67 48.17 36.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR HAS A REDUCED PEPTIDE BOND ISOSTERE REMARK 600 [CH2-NH] IN PLACE OF THE SCISSILE AMIDE REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: N-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL)AMINO] REMARK 630 HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~-[AMINO(IMINIO)METHYL]-L- REMARK 630 ORNITHINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 2NC A 204 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ACE THR ILE 2A0 GLN ARG NH2 REMARK 630 DETAILS: 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 2NC A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O40 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED 203 AMINO ACID ' REMARK 900 COVALENT DIMER' HIV-1 PROTEASE MOLECULE DBREF 3FSM A 1 203 PDB 3FSM 3FSM 1 203 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 MODRES 3FSM NLE A 36 LEU NORLEUCINE MODRES 3FSM YCM A 41 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 3FSM NLE A 46 LEU NORLEUCINE MODRES 3FSM ABA A 67 ALA ALPHA-AMINOBUTYRIC ACID MODRES 3FSM ABA A 95 ALA ALPHA-AMINOBUTYRIC ACID MODRES 3FSM YCM A 100 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 3FSM NLE A 140 LEU NORLEUCINE MODRES 3FSM YCM A 145 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 3FSM NLE A 150 LEU NORLEUCINE MODRES 3FSM ABA A 171 ALA ALPHA-AMINOBUTYRIC ACID MODRES 3FSM ABA A 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 2NC A 204 54 HETNAM NLE NORLEUCINE HETNAM YCM S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HETNAM ABA ALPHA-AMINOBUTYRIC ACID HETNAM DAL D-ALANINE HETNAM 2NC N-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL) HETNAM 2 2NC AMINO]HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~- HETNAM 3 2NC [AMINO(IMINIO)METHYL]-L-ORNITHINAMIDE HETSYN YCM CYSTEINE-S-ACETAMIDE HETSYN 2NC P2/NC FORMUL 1 NLE 4(C6 H13 N O2) FORMUL 1 YCM 3(C5 H10 N2 O3 S) FORMUL 1 ABA 4(C4 H9 N O2) FORMUL 1 DAL C3 H7 N O2 FORMUL 2 2NC C35 H68 N11 O8 1+ FORMUL 3 HOH *118(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 LYS A 43 GLY A 49 0 SHEET 2 B 8 GLY A 52 ILE A 66 -1 O GLN A 58 N LYS A 43 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 GLN A 162 N LYS A 147 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 VAL A 115 O ALA A 126 SHEET 8 C 8 GLY A 156 ILE A 170 -1 O GLU A 169 N ARG A 118 LINK C GLU A 35 N NLE A 36 1555 1555 1.33 LINK C NLE A 36 N ASN A 37 1555 1555 1.33 LINK C GLY A 40 N YCM A 41 1555 1555 1.32 LINK C YCM A 41 N TRP A 42 1555 1555 1.33 LINK C LYS A 45 N NLE A 46 1555 1555 1.34 LINK C NLE A 46 N ILE A 47 1555 1555 1.34 LINK C ILE A 66 N ABA A 67 1555 1555 1.33 LINK C ABA A 67 N GLY A 68 1555 1555 1.33 LINK C GLY A 94 N ABA A 95 1555 1555 1.32 LINK C ABA A 95 N THR A 96 1555 1555 1.35 LINK C PHE A 99 N YCM A 100 1555 1555 1.34 LINK C YCM A 100 N GLY A 101 1555 1555 1.33 LINK C GLU A 139 N NLE A 140 1555 1555 1.33 LINK C NLE A 140 N ASN A 141 1555 1555 1.33 LINK C GLY A 144 N YCM A 145 1555 1555 1.36 LINK C YCM A 145 N TRP A 146 1555 1555 1.32 LINK C LYS A 149 N NLE A 150 1555 1555 1.33 LINK C NLE A 150 N ILE A 151 1555 1555 1.33 LINK C ILE A 154 N DAL A 155 1555 1555 1.35 LINK C DAL A 155 N GLY A 156 1555 1555 1.33 LINK C ILE A 170 N ABA A 171 1555 1555 1.34 LINK C ABA A 171 N GLY A 172 1555 1555 1.33 LINK C GLY A 198 N ABA A 199 1555 1555 1.34 LINK C ABA A 199 N THR A 200 1555 1555 1.33 SITE 1 AC1 7 ALA A 51 GLY A 52 PHE A 53 GLY A 153 SITE 2 AC1 7 ILE A 154 GLY A 156 HOH A 274 SITE 1 AC2 24 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 2 AC2 24 ASP A 30 ILE A 47 GLY A 48 GLY A 49 SITE 3 AC2 24 ILE A 50 VAL A 82 ASP A 129 GLY A 131 SITE 4 AC2 24 ALA A 132 ASP A 133 ASP A 134 GLY A 152 SITE 5 AC2 24 ILE A 154 PRO A 185 VAL A 186 ILE A 188 SITE 6 AC2 24 HOH A 205 HOH A 208 HOH A 248 HOH A 312 CRYST1 51.472 58.286 61.450 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 0.019428 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017157 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016273 0.00000