HEADER IMMUNE SYSTEM 11-MAY-06 2CMR TITLE CRYSTAL STRUCTURE OF THE HIV-1 NEUTRALIZING ANTIBODY D5 FAB BOUND TO TITLE 2 THE GP41 INNER-CORE MIMETIC 5-HELIX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 5-HELIX, RESIDUES 543-582 AND 625-662; COMPND 5 SYNONYM: GP41; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: SEQUENCE DERIVED FROM GENBANK P04578 WHERE THREE COMPND 8 REGIONS EACH EQUIVALENT TO AA 543-582 ARE INTERSPERSED BY TWO COMPND 9 DIFFERENT REGIONS (EACH EQUIVALENT TO AA 625-662). LINKERS GGSGG AND COMPND 10 GSSGG JOIN THE REGIONS AND ALTERNATE STARTING WITH GGSGG. A COMPND 11 METHIONINE INITIATES AND A TAIL CONTAINS GGHHHHHHG; COMPND 12 MOL_ID: 2; COMPND 13 MOLECULE: D5; COMPND 14 CHAIN: H; COMPND 15 SYNONYM: FAB HEAVY CHAIN; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: D5; COMPND 19 CHAIN: L; COMPND 20 SYNONYM: FAB LIGHT CHAIN; COMPND 21 ENGINEERED: 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM_CELL_LINE: 293-EBNA; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PEU3.2, PEU1.2; SOURCE 16 OTHER_DETAILS: IGG DERIVED FROM HUMAN B CELL LIBRARY; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 22 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 24 EXPRESSION_SYSTEM_CELL_LINE: 293-EBNA; SOURCE 25 EXPRESSION_SYSTEM_PLASMID: PEU3.2, PEU1.2; SOURCE 26 OTHER_DETAILS: IGG DERIVED FROM HUMAN B CELL LIBRARY KEYWDS IMMUNE SYSTEM, IMMUNOGLOBULIN COMPLEX, NEUTRALIZATION, KEYWDS 2 IMMUNOGLOBULIN, ENVELOPE PROTEIN, HIV, GP41, AIDS, MHC I, MEMBRANE, KEYWDS 3 TRANSMEMBRANE, IMMUNOGLOBULIN DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.LUFTIG,M.MATTU,P.DI GIOVINE,R.GELEZIUNAS,R.HRIN,G.BARBATO, AUTHOR 2 E.BIANCHI,M.D.MILLER,A.PESSI,A.CARFI REVDAT 4 13-DEC-23 2CMR 1 REMARK REVDAT 3 08-NOV-17 2CMR 1 SOURCE REVDAT 2 24-FEB-09 2CMR 1 VERSN REVDAT 1 16-OCT-06 2CMR 0 JRNL AUTH M.A.LUFTIG,M.MATTU,P.DI GIOVINE,R.GELEZIUNAS,R.HRIN, JRNL AUTH 2 G.BARBATO,E.BIANCHI,M.D.MILLER,A.PESSI,A.CARFI JRNL TITL STRUCTURAL BASIS FOR HIV-1 NEUTRALIZATION BY A GP41 FUSION JRNL TITL 2 INTERMEDIATE-DIRECTED ANTIBODY JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 740 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 16862157 JRNL DOI 10.1038/NSMB1127 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 41190 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2020 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2679 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4674 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : 0.48000 REMARK 3 B33 (A**2) : -0.44000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.88000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.210 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.186 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.936 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4775 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4234 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6483 ; 1.426 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9906 ; 0.832 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 596 ; 6.526 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 742 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5287 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 889 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 906 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4765 ; 0.238 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2910 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 233 ; 0.187 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL 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): 8 ; 0.252 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 67 ; 0.232 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.153 ; 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): 3000 ; 0.827 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4826 ; 1.560 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1775 ; 2.423 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1657 ; 4.019 ; 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 : 1.40 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 2CMR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1290028687. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41190 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 33.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1AIK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% (W/V) PEG 4000, 0.2 M TRI-SODIUM REMARK 280 CITRATE DIHYDRATE, 0.1 M TRIS-HCL / PH = 8.5, PH 8.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 100.82200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.80900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 100.82200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.80900 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L 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 GLY A 43 REMARK 465 SER A 44 REMARK 465 GLY A 45 REMARK 465 GLY A 46 REMARK 465 HIS A 47 REMARK 465 THR A 48 REMARK 465 GLY A 85 REMARK 465 SER A 86 REMARK 465 SER A 87 REMARK 465 GLY A 88 REMARK 465 ALA A 129 REMARK 465 GLY A 130 REMARK 465 GLY A 131 REMARK 465 SER A 132 REMARK 465 GLY A 133 REMARK 465 GLY A 134 REMARK 465 HIS A 135 REMARK 465 THR A 136 REMARK 465 THR A 137 REMARK 465 SER A 174 REMARK 465 SER A 175 REMARK 465 ALA A 217 REMARK 465 GLY A 218 REMARK 465 GLY A 219 REMARK 465 HIS A 220 REMARK 465 HIS A 221 REMARK 465 HIS A 222 REMARK 465 HIS A 223 REMARK 465 HIS A 224 REMARK 465 HIS A 225 REMARK 465 GLY A 226 REMARK 465 GLN H 1 REMARK 465 VAL H 2 REMARK 465 PRO H 126 REMARK 465 CYS H 127 REMARK 465 SER H 128 REMARK 465 ARG H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 REMARK 465 GLY H 133 REMARK 465 SER H 188 REMARK 465 LEU H 189 REMARK 465 GLY H 190 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 MET A 1 CB CG SD CE REMARK 470 GLN A 2 CG CD OE1 NE2 REMARK 470 GLY A 42 CA C O REMARK 470 GLU A 84 CA C O CB CG CD OE1 REMARK 470 GLU A 84 OE2 REMARK 470 GLN A 90 CG CD OE1 NE2 REMARK 470 GLY A 173 CA C O REMARK 470 GLN H 192 CB CG CD OE1 NE2 REMARK 470 ARG H 210 NH1 NH2 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 N GLY A 89 O HOH A 401 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 ARG H 210 NE ARG H 210 CZ 0.171 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 LEU A 83 O - C - N ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG H 66 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG H 94 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG H 94 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ASP H 144 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG H 210 CD - NE - CZ ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG L 107 NE - CZ - NH1 ANGL. DEV. = 3.1 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 GLN H 64 124.30 -37.07 REMARK 500 SER H 76 54.70 33.35 REMARK 500 SER H 82B 55.34 37.21 REMARK 500 TYR L 30 -121.50 58.96 REMARK 500 ALA L 51 -35.61 71.16 REMARK 500 ASN L 137 60.40 66.09 REMARK 500 ASN L 151 -88.62 50.12 REMARK 500 ALA L 152 -51.63 -22.55 REMARK 500 PRO L 203 134.18 -35.73 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 LEU H 124 ALA H 125 -31.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1582 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AIK RELATED DB: PDB REMARK 900 HIV GP41 CORE STRUCTURE REMARK 900 RELATED ID: 1DF4 RELATED DB: PDB REMARK 900 INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR REMARK 900 IMPLICATIONS FOR MEMBRANE FUSION REMARK 900 RELATED ID: 1DF5 RELATED DB: PDB REMARK 900 INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR REMARK 900 IMPLICATIONS FOR MEMBRANE FUSION REMARK 900 RELATED ID: 1DLB RELATED DB: PDB REMARK 900 HELICAL INTERACTIONS IN THE HIV-1 GP41 CORE REVEALS STRUCTURAL REMARK 900 BASIS FOR THE INHIBITORY ACTIVITY OF GP41 PEPTIDES REMARK 900 RELATED ID: 1G9M RELATED DB: PDB REMARK 900 HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4AND REMARK 900 INDUCED NEUTRALIZING ANTIBODY 17B REMARK 900 RELATED ID: 1GC1 RELATED DB: PDB REMARK 900 HIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN REMARK 900 ANTIBODY REMARK 900 RELATED ID: 1GZL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C14LINKMID/IQN17: A CROSS-LINKED INHIBITOR OF REMARK 900 HIV-1 ENTRY BOUND TO THE GP41 HYDROPHOBIC POCKET REMARK 900 RELATED ID: 1K33 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF THE GP41 CORE MUTANT REMARK 900 RELATED ID: 1K34 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF GP41 CORE MUTANT REMARK 900 RELATED ID: 1MZI RELATED DB: PDB REMARK 900 SOLUTION ENSEMBLE STRUCTURES OF HIV-1 GP41 2F5 MAB EPITOPE REMARK 900 RELATED ID: 1OPN RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF CCR5 RECEPTOR IN COMPLEX WITH HIVGP120 REMARK 900 ENVELOPE GLYCOPROTEIN AND CD4 RECEPTOR REMARK 900 RELATED ID: 1OPT RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF CCR5 RECEPTOR IN COMPLEX WITH HIVGP120 REMARK 900 ENVELOPE GLYCOPROTEIN AND CD4 RECEPTOR REMARK 900 RELATED ID: 1OPW RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF CCR5 RECEPTOR IN COMPLEX WITH HIVGP120 REMARK 900 ENVELOPE GLYCOPROTEIN AND CD4 RECEPTOR REMARK 900 RELATED ID: 1RZJ RELATED DB: PDB REMARK 900 HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4AND REMARK 900 INDUCED NEUTRALIZING ANTIBODY 17B DBREF 2CMR A 1 1 PDB 2CMR 2CMR 1 1 DBREF 2CMR A 2 41 UNP P04578 ENV_HV1H2 543 582 DBREF 2CMR A 42 46 PDB 2CMR 2CMR 42 46 DBREF 2CMR A 47 84 UNP P04578 ENV_HV1H2 625 662 DBREF 2CMR A 85 89 PDB 2CMR 2CMR 85 89 DBREF 2CMR A 90 129 UNP P04578 ENV_HV1H2 543 582 DBREF 2CMR A 130 134 PDB 2CMR 2CMR 130 134 DBREF 2CMR A 135 172 UNP P04578 ENV_HV1H2 625 662 DBREF 2CMR A 173 177 PDB 2CMR 2CMR 173 177 DBREF 2CMR A 178 217 UNP P04578 ENV_HV1H2 543 582 DBREF 2CMR A 218 226 PDB 2CMR 2CMR 218 226 DBREF 2CMR H 1 211 PDB 2CMR 2CMR 1 211 DBREF 2CMR L 1 207 PDB 2CMR 2CMR 1 207 SEQRES 1 A 226 MET GLN LEU LEU SER GLY ILE VAL GLN GLN GLN ASN ASN SEQRES 2 A 226 LEU LEU ARG ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN SEQRES 3 A 226 LEU THR VAL TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE SEQRES 4 A 226 LEU ALA GLY GLY SER GLY GLY HIS THR THR TRP MET GLU SEQRES 5 A 226 TRP ASP ARG GLU ILE ASN ASN TYR THR SER LEU ILE HIS SEQRES 6 A 226 SER LEU ILE GLU GLU SER GLN ASN GLN GLN GLU LYS ASN SEQRES 7 A 226 GLU GLN GLU LEU LEU GLU GLY SER SER GLY GLY GLN LEU SEQRES 8 A 226 LEU SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 9 A 226 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 10 A 226 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU ALA GLY SEQRES 11 A 226 GLY SER GLY GLY HIS THR THR TRP MET GLU TRP ASP ARG SEQRES 12 A 226 GLU ILE ASN ASN TYR THR SER LEU ILE HIS SER LEU ILE SEQRES 13 A 226 GLU GLU SER GLN ASN GLN GLN GLU LYS ASN GLU GLN GLU SEQRES 14 A 226 LEU LEU GLU GLY SER SER GLY GLY GLN LEU LEU SER GLY SEQRES 15 A 226 ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG ALA ILE GLU SEQRES 16 A 226 ALA GLN GLN HIS LEU LEU GLN LEU THR VAL TRP GLY ILE SEQRES 17 A 226 LYS GLN LEU GLN ALA ARG ILE LEU ALA GLY GLY HIS HIS SEQRES 18 A 226 HIS HIS HIS HIS GLY SEQRES 1 H 217 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL ARG LYS SEQRES 2 H 217 PRO GLY ALA SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 H 217 ASP THR PHE SER SER TYR ALA ILE SER TRP VAL ARG GLN SEQRES 4 H 217 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY GLY ILE ILE SEQRES 5 H 217 PRO ILE PHE GLY THR ALA ASN TYR ALA GLN ALA PHE GLN SEQRES 6 H 217 GLY ARG VAL THR ILE THR ALA ASN GLU SER THR SER THR SEQRES 7 H 217 ALA TYR MET GLU LEU SER SER LEU ARG SER GLU ASP THR SEQRES 8 H 217 ALA ILE TYR TYR CYS ALA ARG ASP ASN PRO THR LEU LEU SEQRES 9 H 217 GLY SER ASP TYR TRP GLY ALA GLY THR LEU VAL THR VAL SEQRES 10 H 217 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 H 217 ALA PRO CYS SER ARG SER THR SER GLY GLY THR ALA ALA SEQRES 12 H 217 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 H 217 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 H 217 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 H 217 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 H 217 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 H 217 SER ASN THR LYS VAL ASP LYS ARG VAL SEQRES 1 L 208 ASP ILE GLN MET THR GLN SER PRO SER THR LEU SER ALA SEQRES 2 L 208 SER ILE GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 208 GLU GLY ILE TYR HIS TRP LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 208 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR LYS ALA SER SEQRES 5 L 208 SER LEU ALA SER GLY ALA PRO SER ARG PHE SER GLY SER SEQRES 6 L 208 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 208 GLN PRO ASP ASP PHE ALA THR TYR TYR CYS GLN GLN TYR SEQRES 8 L 208 SER ASN TYR PRO LEU THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 L 208 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 208 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 208 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 208 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 208 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 208 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 208 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 208 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER HET GOL A 301 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *283(H2 O) HELIX 1 1 MET A 1 ALA A 41 1 41 HELIX 2 2 THR A 49 LEU A 83 1 35 HELIX 3 3 GLY A 89 ILE A 127 1 39 HELIX 4 4 TRP A 138 GLU A 172 1 35 HELIX 5 5 GLN A 178 LEU A 216 1 39 HELIX 6 6 SER H 25 TYR H 32 1 8 HELIX 7 7 GLN H 61 GLN H 64 5 4 HELIX 8 8 GLU H 73 THR H 75 5 3 HELIX 9 9 ARG H 83 THR H 87 5 5 HELIX 10 10 SER H 156 ALA H 158 5 3 HELIX 11 11 GLN L 79 PHE L 83 5 5 HELIX 12 12 SER L 120 LYS L 125 1 6 HELIX 13 13 LYS L 182 HIS L 188 1 7 SHEET 1 HA 4 VAL H 5 GLN H 6 0 SHEET 2 HA 4 VAL H 18 LYS H 23 -1 O LYS H 23 N VAL H 5 SHEET 3 HA 4 THR H 77 LEU H 82 -1 O ALA H 78 N CYS H 22 SHEET 4 HA 4 VAL H 67 ASN H 72 -1 O THR H 68 N GLU H 81 SHEET 1 HB 6 GLU H 10 ARG H 12 0 SHEET 2 HB 6 THR H 107 VAL H 111 1 O LEU H 108 N GLU H 10 SHEET 3 HB 6 ALA H 88 ASN H 96 -1 O ALA H 88 N VAL H 109 SHEET 4 HB 6 ALA H 33 GLN H 39 -1 O ALA H 33 N ASP H 95 SHEET 5 HB 6 GLU H 46 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 HB 6 ALA H 57 TYR H 59 -1 O ASN H 58 N GLY H 50 SHEET 1 HC 4 GLU H 10 ARG H 12 0 SHEET 2 HC 4 THR H 107 VAL H 111 1 O LEU H 108 N GLU H 10 SHEET 3 HC 4 ALA H 88 ASN H 96 -1 O ALA H 88 N VAL H 109 SHEET 4 HC 4 GLY H 100A TRP H 103 -1 O GLY H 100A N ASN H 96 SHEET 1 HD 4 SER H 120 LEU H 124 0 SHEET 2 HD 4 THR H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 HD 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 HD 4 VAL H 163 THR H 165 -1 O HIS H 164 N VAL H 181 SHEET 1 HE 4 SER H 120 LEU H 124 0 SHEET 2 HE 4 THR H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 HE 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 HE 4 VAL H 169 LEU H 170 -1 O VAL H 169 N SER H 177 SHEET 1 HF 3 THR H 151 TRP H 154 0 SHEET 2 HF 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 HF 3 THR H 205 ARG H 210 -1 O THR H 205 N HIS H 200 SHEET 1 LA 4 MET L 4 SER L 7 0 SHEET 2 LA 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 LA 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 LA 4 PHE L 62 SER L 67 -1 O SER L 63 N THR L 74 SHEET 1 LB 6 THR L 10 ALA L 13 0 SHEET 2 LB 6 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 LB 6 THR L 85 GLN L 90 -1 O TYR L 86 N THR L 102 SHEET 4 LB 6 LEU L 33 GLN L 38 -1 O ALA L 34 N GLN L 89 SHEET 5 LB 6 LYS L 45 TYR L 49 -1 O LYS L 45 N GLN L 37 SHEET 6 LB 6 SER L 53 LEU L 54 -1 O SER L 53 N TYR L 49 SHEET 1 LC 4 THR L 10 ALA L 13 0 SHEET 2 LC 4 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 LC 4 THR L 85 GLN L 90 -1 O TYR L 86 N THR L 102 SHEET 4 LC 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 LD 4 SER L 113 PHE L 117 0 SHEET 2 LD 4 THR L 128 PHE L 138 -1 O VAL L 132 N PHE L 117 SHEET 3 LD 4 TYR L 172 SER L 181 -1 O TYR L 172 N PHE L 138 SHEET 4 LD 4 SER L 158 VAL L 162 -1 O GLN L 159 N THR L 177 SHEET 1 LE 4 LEU L 153 GLN L 154 0 SHEET 2 LE 4 TRP L 147 VAL L 149 -1 O VAL L 149 N LEU L 153 SHEET 3 LE 4 TYR L 191 VAL L 195 -1 O ALA L 192 N LYS L 148 SHEET 4 LE 4 VAL L 204 LYS L 206 -1 O VAL L 204 N VAL L 195 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.05 SSBOND 2 CYS H 140 CYS H 196 1555 1555 2.04 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.10 SSBOND 4 CYS L 133 CYS L 193 1555 1555 2.04 CISPEP 1 PHE H 146 PRO H 147 0 -2.80 CISPEP 2 GLU H 148 PRO H 149 0 -8.56 CISPEP 3 SER L 7 PRO L 8 0 -13.14 CISPEP 4 TYR L 94 PRO L 95 0 1.02 CISPEP 5 TYR L 139 PRO L 140 0 1.66 SITE 1 AC1 9 ILE A 145 ASN A 146 GLN A 202 TRP A 206 SITE 2 AC1 9 LYS A 209 HOH A 414 LEU H 100 TRP L 32 SITE 3 AC1 9 TYR L 91 CRYST1 201.644 41.618 90.726 90.00 110.55 90.00 C 1 2 1 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 0.004959 0.000000 0.001859 0.00000 SCALE2 0.000000 0.024028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011771 0.00000