HEADER VIRAL PROTEIN 09-FEB-09 3G7A TITLE HIV GP41 SIX-HELIX BUNDLE COMPOSED OF A CHIMERIC ALPHA+ALPHA/BETA- TITLE 2 PEPTIDE ANALOGUE OF THE CHR DOMAIN IN COMPLEX WITH AN NHR DOMAIN TITLE 3 ALPHA-PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP160; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENV POLYPROTEIN, SURFACE PROTEIN, SU, GLYCOPROTEIN 120, COMPND 5 GP120, TRANSMEMBRANE PROTEIN, TM, GLYCOPROTEIN 41, GP41; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CHIMERIC ALPHA+ALPHA/BETA-PEPTIDE ANALOGUE OF THE HIV GP41 COMPND 9 CHR DOMAIN; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC PEPTIDE; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS HIV, VIRAL FUSION, GP41, HELIX-BUNDLE, ALPHA/BETA-PEPTIDE, FOLDAMER, KEYWDS 2 AIDS, APOPTOSIS, CELL MEMBRANE, CLEAVAGE ON PAIR OF BASIC RESIDUES, KEYWDS 3 ENVELOPE PROTEIN, FUSION PROTEIN, GLYCOPROTEIN, HOST-VIRUS KEYWDS 4 INTERACTION, LIPOPROTEIN, MEMBRANE, PALMITATE, TRANSMEMBRANE, VIRAL KEYWDS 5 IMMUNOEVASION, VIRION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.S.HORNE,L.M.JOHNSON,S.H.GELLMAN REVDAT 4 15-NOV-23 3G7A 1 ATOM REVDAT 3 06-SEP-23 3G7A 1 REMARK LINK REVDAT 2 13-JUL-11 3G7A 1 VERSN REVDAT 1 20-OCT-09 3G7A 0 JRNL AUTH W.S.HORNE,L.M.JOHNSON,T.J.KETAS,P.J.KLASSE,M.LU,J.P.MOORE, JRNL AUTH 2 S.H.GELLMAN JRNL TITL STRUCTURAL AND BIOLOGICAL MIMICRY OF PROTEIN SURFACE JRNL TITL 2 RECOGNITION BY ALPHA/BETA-PEPTIDE FOLDAMERS JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 14751 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19706443 JRNL DOI 10.1073/PNAS.0902663106 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 2947 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) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.311 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.300 REMARK 3 FREE R VALUE TEST SET COUNT : 132 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 208 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4550 REMARK 3 BIN FREE R VALUE SET COUNT : 5 REMARK 3 BIN FREE R VALUE : 0.4620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 574 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 12 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) : 32.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.54000 REMARK 3 B22 (A**2) : 3.54000 REMARK 3 B33 (A**2) : -5.31000 REMARK 3 B12 (A**2) : 1.77000 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): 0.797 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.403 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.329 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.290 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 608 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 417 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 820 ; 1.751 ; 2.038 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1026 ; 0.970 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 57 ; 5.362 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 26 ;32.576 ;26.538 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 92 ;21.476 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;14.274 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 95 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 603 ; 0.004 ; 0.018 REMARK 3 GENERAL PLANES OTHERS (A): 100 ; 0.001 ; 0.017 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 369 ; 5.461 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 150 ; 2.261 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 582 ; 7.709 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 239 ; 4.422 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 238 ; 7.095 ; 3.000 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 36 REMARK 3 RESIDUE RANGE : B 2 B 38 REMARK 3 ORIGIN FOR THE GROUP (A): 20.4520 -17.2340 5.5760 REMARK 3 T TENSOR REMARK 3 T11: 0.0391 T22: 0.3342 REMARK 3 T33: 0.0104 T12: 0.0312 REMARK 3 T13: -0.0074 T23: 0.0181 REMARK 3 L TENSOR REMARK 3 L11: 2.6820 L22: 2.5328 REMARK 3 L33: 0.8075 L12: 0.5016 REMARK 3 L13: -1.0340 L23: -1.1693 REMARK 3 S TENSOR REMARK 3 S11: 0.0671 S12: -0.1593 S13: -0.1115 REMARK 3 S21: 0.0284 S22: -0.0662 S23: -0.1297 REMARK 3 S31: -0.0705 S32: -0.0345 S33: -0.0009 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 4 REMARK 4 3G7A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051512. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GOBEL MIRRORS REMARK 200 OPTICS : CONFOCAL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3085 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38800 REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRIES 3F4Y, 3F50 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M LITHIUM SULFATE, 12% W/V PEG REMARK 280 8000, 20% V/V GLYCEROL, PH 7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 28.52150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 16.46690 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 62.10467 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 28.52150 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 16.46690 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 62.10467 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 28.52150 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 16.46690 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 62.10467 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 28.52150 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 16.46690 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 62.10467 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 28.52150 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 16.46690 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 62.10467 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 28.52150 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 16.46690 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 62.10467 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 32.93379 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 124.20933 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 32.93379 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 124.20933 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 32.93379 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 124.20933 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 32.93379 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 124.20933 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 32.93379 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 124.20933 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 32.93379 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 124.20933 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 28.52150 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -49.40069 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 57.04300 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 THR B 1 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 GLN A 5 CG CD OE1 NE2 REMARK 470 GLN A 32 CD OE1 NE2 REMARK 470 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 35 CG1 CG2 CD1 REMARK 470 LEU A 36 CG CD1 CD2 REMARK 470 ARG B 16 CZ NH1 NH2 REMARK 470 B3E B 29 CE OF2 OF1 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 XCP B 19 C - N - CA ANGL. DEV. = 20.1 DEGREES REMARK 500 XCP B 33 C - N - CA ANGL. DEV. = 22.8 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 ILE A 35 47.96 -89.44 REMARK 500 ALA B 24 -72.16 -62.47 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 ALA B 14 XCP B 15 142.49 REMARK 500 GLU B 18 XCP B 19 145.72 REMARK 500 ILE B 21 XPC B 22 141.61 REMARK 500 B3E B 26 GLN B 27 136.33 REMARK 500 B3E B 29 LYS B 30 144.91 REMARK 500 GLU B 32 XCP B 33 149.59 REMARK 500 LEU B 35 XPC B 36 140.75 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 B3E B 26 -20.24 REMARK 500 B3E B 29 -16.64 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 ACE A 0 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 37 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 38 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 39 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 40 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F4Y RELATED DB: PDB REMARK 900 HIV GP41 SIX-HELIX BUNDLE WITH MUTATED CHR SEQUENCE REMARK 900 RELATED ID: 3F50 RELATED DB: PDB REMARK 900 HIV GP41 SIX-HELIX BUNDLE WITH AN ALPHA/BETA-PEPTIDE CHR ANALOGUE REMARK 900 RELATED ID: 1AIK RELATED DB: PDB REMARK 900 HIV GP41 SIX-HELIX BUNDLE STRUCTURE WITH NATIVE CHR SEQUENCE DBREF 3G7A A 1 36 UNP P04580 ENV_HV1Z6 545 580 DBREF 3G7A B 1 38 PDB 3G7A 3G7A 1 38 SEQRES 1 A 36 SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG ALA SEQRES 2 A 36 ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL TRP SEQRES 3 A 36 GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU SEQRES 1 B 38 THR THR TRP GLU ALA TRP ASP ARG ALA ILE ALA GLU TYR SEQRES 2 B 38 ALA XCP ARG ILE GLU XCP LEU ILE XPC ALA ALA GLN B3E SEQRES 3 B 38 GLN GLN B3E LYS ASN GLU XCP ALA LEU XPC GLU LEU MODRES 3G7A B3E B 26 GLU (3S)-3-AMINOHEXANEDIOIC ACID MODRES 3G7A B3E B 29 GLU (3S)-3-AMINOHEXANEDIOIC ACID HET XCP B 15 17 HET XCP B 19 17 HET XPC B 22 17 HET B3E B 26 18 HET B3E B 29 15 HET XCP B 33 17 HET XPC B 36 17 HET ACE A 0 6 HET GOL A 37 14 HET GOL A 38 14 HET GOL B 39 14 HET GOL B 40 14 HETNAM XCP (1S,2S)-2-AMINOCYCLOPENTANECARBOXYLIC ACID HETNAM XPC (3S,4R)-4-AMINOPYRROLIDINE-3-CARBOXYLIC ACID HETNAM B3E (3S)-3-AMINOHEXANEDIOIC ACID HETNAM ACE ACETYL GROUP HETNAM GOL GLYCEROL HETSYN XPC (3R,4S)-3-AMINOPYRROLIDINE-4-CARBOXYLIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 XCP 3(C6 H11 N O2) FORMUL 2 XPC 2(C5 H10 N2 O2) FORMUL 2 B3E 2(C6 H11 N O4) FORMUL 3 ACE C2 H4 O FORMUL 4 GOL 4(C3 H8 O3) FORMUL 8 HOH *12(H2 O) HELIX 1 1 SER A 1 ILE A 35 1 35 HELIX 2 2 THR B 2 LEU B 38 1 37 LINK C ACE A 0 N SER A 1 1555 1555 1.34 LINK C ALA B 14 N XCP B 15 1555 1555 1.31 LINK C XCP B 15 N ARG B 16 1555 1555 1.32 LINK C GLU B 18 N XCP B 19 1555 1555 1.33 LINK C XCP B 19 N LEU B 20 1555 1555 1.32 LINK C ILE B 21 N XPC B 22 1555 1555 1.29 LINK C XPC B 22 N ALA B 23 1555 1555 1.33 LINK C GLN B 25 N B3E B 26 1555 1555 1.34 LINK C B3E B 26 N GLN B 27 1555 1555 1.34 LINK C GLN B 28 N B3E B 29 1555 1555 1.28 LINK C B3E B 29 N LYS B 30 1555 1555 1.34 LINK C GLU B 32 N XCP B 33 1555 1555 1.34 LINK C XCP B 33 N ALA B 34 1555 1555 1.34 LINK C LEU B 35 N XPC B 36 1555 1555 1.30 LINK C XPC B 36 N GLU B 37 1555 1555 1.34 SITE 1 AC1 4 SER A 1 GLY A 2 ILE A 3 VAL A 4 SITE 1 AC2 4 ARG A 12 THR B 2 GLU B 4 ARG B 8 SITE 1 AC3 2 GLU A 15 HOH A 39 SITE 1 AC4 1 LYS A 29 SITE 1 AC5 3 GLU B 12 TYR B 13 ARG B 16 CRYST1 57.043 57.043 186.314 90.00 90.00 120.00 H 3 2 18 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 0.017531 0.010121 0.000000 0.00000 SCALE2 0.000000 0.020243 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005367 0.00000