HEADER IMMUNE SYSTEM 04-NOV-13 4NHC TITLE CRYSTAL STRUCTURE OF THE HIV-1 NEUTRALIZING ANTIBODY 4E10 FAB FRAGMENT TITLE 2 IN COMPLEX WITH A HYDROCARBON-STAPLED PEPTIDE CONTAINING THE 4E10 TITLE 3 EPITOPE ON GP41. COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: MODIFIED FRAGMENT OF HIV GLYCOPROTEIN (GP41); COMPND 11 CHAIN: P; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: CHO CELLS; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: CHO CELLS; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: SYNTHETIC; THIS SEQUENCE INCLUDES A MODIFIED FRAGMENT SOURCE 16 OF THE HIV ENVELOPE PROTEIN GP41 KEYWDS IMMUNOGLOBULIN FOLD, BETA-SANDWICH, 4E10 FAB, ANTIBODY-EPITOPE KEYWDS 2 COMPLEX, GP41 HIV-1, HYDROCARBON STAPLE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.IRIMIA,I.A.WILSON REVDAT 4 06-DEC-23 4NHC 1 REMARK REVDAT 3 20-SEP-23 4NHC 1 REMARK LINK REVDAT 2 24-DEC-14 4NHC 1 JRNL REVDAT 1 03-DEC-14 4NHC 0 JRNL AUTH G.H.BIRD,A.IRIMIA,G.OFEK,P.D.KWONG,I.A.WILSON,L.D.WALENSKY JRNL TITL STAPLED HIV-1 PEPTIDES RECAPITULATE ANTIGENIC STRUCTURES AND JRNL TITL 2 ENGAGE BROADLY NEUTRALIZING ANTIBODIES. JRNL REF NAT.STRUCT.MOL.BIOL. V. 21 1058 2014 JRNL REFN ISSN 1545-9993 JRNL PMID 25420104 JRNL DOI 10.1038/NSMB.2922 REMARK 2 REMARK 2 RESOLUTION. 2.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 13737 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.9605 - 4.9781 1.00 2904 154 0.2106 0.2523 REMARK 3 2 4.9781 - 3.9518 1.00 2730 144 0.1677 0.2243 REMARK 3 3 3.9518 - 3.4524 1.00 2677 141 0.2075 0.2848 REMARK 3 4 3.4524 - 3.1368 0.97 2617 137 0.2475 0.3096 REMARK 3 5 3.1368 - 2.9120 0.80 2121 112 0.3118 0.3939 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 48.06 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 63.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -12.82380 REMARK 3 B22 (A**2) : -12.82380 REMARK 3 B33 (A**2) : 25.64750 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3710 REMARK 3 ANGLE : 0.793 4905 REMARK 3 CHIRALITY : 0.050 546 REMARK 3 PLANARITY : 0.003 628 REMARK 3 DIHEDRAL : 15.269 1288 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'L' AND ((RESSEQ 1:108)) REMARK 3 ORIGIN FOR THE GROUP (A): 66.6637 -77.5302 -0.6100 REMARK 3 T TENSOR REMARK 3 T11: 0.5036 T22: 0.4851 REMARK 3 T33: 0.6031 T12: -0.0302 REMARK 3 T13: 0.1004 T23: 0.0961 REMARK 3 L TENSOR REMARK 3 L11: 1.0952 L22: 0.9227 REMARK 3 L33: 0.2962 L12: -0.3546 REMARK 3 L13: -0.4866 L23: 0.0580 REMARK 3 S TENSOR REMARK 3 S11: -0.3144 S12: 0.0666 S13: -0.4310 REMARK 3 S21: 0.0556 S22: 0.2269 S23: 0.3798 REMARK 3 S31: 0.3578 S32: -0.0754 S33: -0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'L' AND ((RESSEQ 109:214)) REMARK 3 ORIGIN FOR THE GROUP (A): 40.7978 -52.7525 5.1576 REMARK 3 T TENSOR REMARK 3 T11: 0.3976 T22: 0.4634 REMARK 3 T33: 0.5295 T12: -0.0350 REMARK 3 T13: -0.0148 T23: 0.1127 REMARK 3 L TENSOR REMARK 3 L11: 0.7177 L22: 0.4787 REMARK 3 L33: 0.5487 L12: 0.0510 REMARK 3 L13: -0.6483 L23: -0.1105 REMARK 3 S TENSOR REMARK 3 S11: -0.0911 S12: 0.0794 S13: 0.0681 REMARK 3 S21: 0.1117 S22: 0.0948 S23: 0.1730 REMARK 3 S31: -0.0889 S32: -0.1044 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'H' AND ((RESSEQ 1:113)) REMARK 3 ORIGIN FOR THE GROUP (A): 78.0675 -61.0961 -9.5039 REMARK 3 T TENSOR REMARK 3 T11: 0.3199 T22: 0.3860 REMARK 3 T33: 0.3979 T12: -0.0388 REMARK 3 T13: 0.0542 T23: 0.0289 REMARK 3 L TENSOR REMARK 3 L11: 0.3009 L22: 1.2920 REMARK 3 L33: 0.8355 L12: 0.2029 REMARK 3 L13: -0.1615 L23: 0.0340 REMARK 3 S TENSOR REMARK 3 S11: -0.1036 S12: 0.1086 S13: 0.1405 REMARK 3 S21: -0.1870 S22: 0.2677 S23: -0.1243 REMARK 3 S31: -0.0834 S32: -0.0248 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND ((RESSEQ 114:228)) REMARK 3 ORIGIN FOR THE GROUP (A): 53.5042 -45.4814 10.3226 REMARK 3 T TENSOR REMARK 3 T11: 0.4723 T22: 0.5507 REMARK 3 T33: 0.5022 T12: -0.0847 REMARK 3 T13: -0.0140 T23: 0.0846 REMARK 3 L TENSOR REMARK 3 L11: 0.3524 L22: 0.8466 REMARK 3 L33: 0.3406 L12: 0.5131 REMARK 3 L13: -0.1810 L23: -0.4454 REMARK 3 S TENSOR REMARK 3 S11: 0.0804 S12: -0.1782 S13: 0.1346 REMARK 3 S21: 0.1075 S22: -0.3398 S23: -0.2197 REMARK 3 S31: -0.1555 S32: 0.0820 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'P' AND ((RESSEQ 670:686)) REMARK 3 ORIGIN FOR THE GROUP (A): 90.7667 -77.3818 -12.5171 REMARK 3 T TENSOR REMARK 3 T11: 0.5446 T22: 0.3659 REMARK 3 T33: 0.6260 T12: 0.0353 REMARK 3 T13: 0.1611 T23: 0.0758 REMARK 3 L TENSOR REMARK 3 L11: 2.6733 L22: 1.4702 REMARK 3 L33: 2.2601 L12: -1.7928 REMARK 3 L13: 0.7810 L23: 0.2120 REMARK 3 S TENSOR REMARK 3 S11: 0.5057 S12: -0.3197 S13: -0.9156 REMARK 3 S21: -0.8039 S22: -0.3752 S23: 0.2099 REMARK 3 S31: 0.3412 S32: -0.5660 S33: -0.0140 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4NHC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 2 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) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR, REMARK 200 SI(111) REMARK 200 OPTICS : 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 : 13767 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.910 REMARK 200 RESOLUTION RANGE LOW (A) : 48.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 21.90 REMARK 200 R MERGE (I) : 0.18200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.66600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 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 ENTRY 2FX7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION: 0.2 M NACL, 0.1 M REMARK 280 NA/K PHOSPHATE PH 6.2, 50% PEG 200, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 22K, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 13.94133 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 27.88267 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.91200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.85333 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 6.97067 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 13.94133 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 27.88267 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.85333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 20.91200 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 6.97067 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, P 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 THE STAPLED PEPTIDES IN THE STRUCTURE WAS OBTAINED BY INCORPORATION REMARK 400 OF (R)-2-(((9H-FLUOREN-9-YL)METHOXY)CARBONYLAMINO)-2-METHYL-PENT-4- REMARK 400 ENOIC ACID AT THE POSITION 678 AND (S)-2-(((9H-FLUOREN-9-YL)METHOXY) REMARK 400 CARBONYLAMINO)-2-METHYL-HEPT-6-ENOIC ACID AT THE POSITION 681 REMARK 400 REMARK 400 THE STAPLED PEPTIDE (ACE)NWFNITN(DIV)LW(MK8)IKKKK IS PEPTIDE-LIKE, REMARK 400 A MEMBER OF UNKNOWN CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: STAPLED PEPTIDE (ACE)NWFNITN(DIV)LW(MK8)IKKKK REMARK 400 CHAIN: P REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: MODIFIED FRAGMENT OF HIV GLYCOPROTEIN (GP41) 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 TRP P 680 C MK8 P 681 N 0.153 REMARK 500 MK8 P 681 C ILE P 682 N 0.155 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 ACE P 670 O - C - N ANGL. DEV. = 12.9 DEGREES REMARK 500 ASN P 671 C - N - CA ANGL. DEV. = -19.2 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 ASN L 30 19.43 54.63 REMARK 500 PRO L 40 -79.85 -19.90 REMARK 500 ALA L 51 -46.19 73.40 REMARK 500 ALA L 84 -159.80 -150.68 REMARK 500 ASN L 138 61.80 65.47 REMARK 500 PRO L 141 -167.51 -71.92 REMARK 500 ASN L 152 -8.32 72.95 REMARK 500 LYS L 190 -80.33 -88.95 REMARK 500 ARG L 211 102.72 -47.35 REMARK 500 VAL H 2 79.42 61.39 REMARK 500 SER H 16 -175.86 -66.48 REMARK 500 VAL H 51 137.61 -171.11 REMARK 500 LEU H 53 -77.48 -49.80 REMARK 500 ARG H 66 -15.35 177.31 REMARK 500 THR H 87 109.09 -59.90 REMARK 500 TRP H 100 50.45 -66.72 REMARK 500 TRP H 100B -111.17 -132.98 REMARK 500 LYS H 100E 104.70 99.96 REMARK 500 PHE H 148 137.71 -179.49 REMARK 500 PRO H 149 -159.78 -93.46 REMARK 500 LYS H 218 83.17 -154.13 REMARK 500 PRO H 227 158.50 -39.75 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 DIV P 678 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TFA L 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TFA H 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NGH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HIV-1 NEUTRALIZING ANTIBODY 4E10 FAB REMARK 900 FRAGMENT IN COMPLEX WITH A HYDROCARBON-STAPLED PEPTIDE CONTAINING REMARK 900 THE 4E10 EPITOPE ON GP41 AND A TETHERED PHOSPHATE MOIETY. DBREF 4NHC L 1 214 PDB 4NHC 4NHC 1 214 DBREF 4NHC H 1 228 PDB 4NHC 4NHC 1 228 DBREF 4NHC P 670 686 PDB 4NHC 4NHC 670 686 SEQRES 1 L 215 GLU ILE VAL LEU THR GLN SER PRO GLY THR GLN SER LEU SEQRES 2 L 215 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 215 GLN SER VAL GLY ASN ASN LYS LEU ALA TRP TYR GLN GLN SEQRES 4 L 215 ARG PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SEQRES 5 L 215 SER SER ARG PRO SER GLY VAL ALA ASP ARG PHE SER GLY SEQRES 6 L 215 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 L 215 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 L 215 TYR GLY GLN SER LEU SER THR PHE GLY GLN GLY THR LYS SEQRES 9 L 215 VAL GLU VAL LYS ARG THR VAL ALA ALA PRO SER VAL PHE SEQRES 10 L 215 ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR SEQRES 11 L 215 ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG SEQRES 12 L 215 GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SEQRES 13 L 215 SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER SEQRES 14 L 215 LYS ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SEQRES 15 L 215 SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS SEQRES 16 L 215 GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SEQRES 17 L 215 SER PHE ASN ARG GLY GLU CYS SEQRES 1 H 228 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS ARG SEQRES 2 H 228 PRO GLY SER SER VAL THR VAL SER CYS LYS ALA SER GLY SEQRES 3 H 228 GLY SER PHE SER THR TYR ALA LEU SER TRP VAL ARG GLN SEQRES 4 H 228 ALA PRO GLY ARG GLY LEU GLU TRP MET GLY GLY VAL ILE SEQRES 5 H 228 PRO LEU LEU THR ILE THR ASN TYR ALA PRO ARG PHE GLN SEQRES 6 H 228 GLY ARG ILE THR ILE THR ALA ASP ARG SER THR SER THR SEQRES 7 H 228 ALA TYR LEU GLU LEU ASN SER LEU ARG PRO GLU ASP THR SEQRES 8 H 228 ALA VAL TYR TYR CYS ALA ARG GLU GLY THR THR GLY TRP SEQRES 9 H 228 GLY TRP LEU GLY LYS PRO ILE GLY ALA PHE ALA HIS TRP SEQRES 10 H 228 GLY GLN GLY THR LEU VAL THR VAL SER SER ALA SER THR SEQRES 11 H 228 LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SEQRES 12 H 228 SER THR SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL SEQRES 13 H 228 LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SEQRES 14 H 228 SER GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA SEQRES 15 H 228 VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SER VAL SEQRES 16 H 228 VAL THR VAL PRO SER SER SER LEU GLY THR GLN THR TYR SEQRES 17 H 228 ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL SEQRES 18 H 228 ASP LYS LYS VAL GLU PRO LYS SEQRES 1 P 17 ACE ASN TRP PHE ASN ILE THR ASN DIV LEU TRP MK8 ILE SEQRES 2 P 17 LYS LYS LYS LYS MODRES 4NHC MK8 P 681 LEU 2-METHYL-L-NORLEUCINE HET ACE P 670 3 HET DIV P 678 7 HET MK8 P 681 9 HET TFA L 301 7 HET PO4 H 301 5 HET TFA H 302 7 HETNAM ACE ACETYL GROUP HETNAM DIV D-ISOVALINE HETNAM MK8 2-METHYL-L-NORLEUCINE HETNAM TFA TRIFLUOROACETIC ACID HETNAM PO4 PHOSPHATE ION FORMUL 3 ACE C2 H4 O FORMUL 3 DIV C5 H11 N O2 FORMUL 3 MK8 C7 H15 N O2 FORMUL 4 TFA 2(C2 H F3 O2) FORMUL 5 PO4 O4 P 3- FORMUL 7 HOH *29(H2 O) HELIX 1 1 VAL L 28 ASN L 31 5 4 HELIX 2 2 GLU L 79 PHE L 83 5 5 HELIX 3 3 SER L 121 LYS L 126 1 6 HELIX 4 4 LYS L 183 GLU L 187 1 5 HELIX 5 5 ARG H 83 THR H 87 5 5 HELIX 6 6 SER H 163 ALA H 165 5 3 HELIX 7 7 SER H 196 LEU H 198 5 3 HELIX 8 8 HIS H 212 ASN H 216 5 5 HELIX 9 9 ASN P 674 LYS P 686 1 13 SHEET 1 A 4 LEU L 4 SER L 7 0 SHEET 2 A 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 A 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 A 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 B 5 THR L 10 LEU L 13 0 SHEET 2 B 5 THR L 102 VAL L 106 1 O GLU L 105 N LEU L 13 SHEET 3 B 5 VAL L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 B 5 LEU L 33 GLN L 38 -1 N GLN L 38 O VAL L 85 SHEET 5 B 5 ARG L 45 ILE L 48 -1 O LEU L 47 N TRP L 35 SHEET 1 C 4 THR L 10 LEU L 13 0 SHEET 2 C 4 THR L 102 VAL L 106 1 O GLU L 105 N LEU L 13 SHEET 3 C 4 VAL L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 C 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 D 4 SER L 114 PHE L 118 0 SHEET 2 D 4 THR L 129 PHE L 139 -1 O VAL L 133 N PHE L 118 SHEET 3 D 4 TYR L 173 SER L 182 -1 O LEU L 175 N LEU L 136 SHEET 4 D 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 E 4 ALA L 153 LEU L 154 0 SHEET 2 E 4 ALA L 144 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 E 4 VAL L 191 HIS L 198 -1 O ALA L 193 N LYS L 149 SHEET 4 E 4 VAL L 205 ASN L 210 -1 O PHE L 209 N TYR L 192 SHEET 1 F 4 GLN H 3 GLN H 6 0 SHEET 2 F 4 VAL H 18 SER H 25 -1 O SER H 25 N GLN H 3 SHEET 3 F 4 THR H 77 LEU H 82 -1 O LEU H 82 N VAL H 18 SHEET 4 F 4 ILE H 67 ALA H 71 -1 N THR H 68 O GLU H 81 SHEET 1 G 6 GLU H 10 LYS H 12 0 SHEET 2 G 6 THR H 107 VAL H 111 1 O LEU H 108 N GLU H 10 SHEET 3 G 6 ALA H 88 THR H 97 -1 N TYR H 90 O THR H 107 SHEET 4 G 6 LEU H 34 GLN H 39 -1 N SER H 35 O ALA H 93 SHEET 5 G 6 LEU H 45 ILE H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 G 6 ILE H 56 TYR H 59 -1 O ILE H 56 N ILE H 52 SHEET 1 H 4 GLU H 10 LYS H 12 0 SHEET 2 H 4 THR H 107 VAL H 111 1 O LEU H 108 N GLU H 10 SHEET 3 H 4 ALA H 88 THR H 97 -1 N TYR H 90 O THR H 107 SHEET 4 H 4 PRO H 100F TRP H 103 -1 O HIS H 102 N ARG H 94 SHEET 1 I 4 SER H 120 LEU H 124 0 SHEET 2 I 4 THR H 137 TYR H 147 -1 O LYS H 145 N SER H 120 SHEET 3 I 4 TYR H 185 PRO H 194 -1 O TYR H 185 N TYR H 147 SHEET 4 I 4 VAL H 171 THR H 173 -1 N HIS H 172 O VAL H 190 SHEET 1 J 4 THR H 133 SER H 134 0 SHEET 2 J 4 THR H 137 TYR H 147 -1 O THR H 137 N SER H 134 SHEET 3 J 4 TYR H 185 PRO H 194 -1 O TYR H 185 N TYR H 147 SHEET 4 J 4 VAL H 177 LEU H 178 -1 N VAL H 177 O SER H 186 SHEET 1 K 3 THR H 153 TRP H 157 0 SHEET 2 K 3 TYR H 206 ASN H 211 -1 O ASN H 209 N SER H 156 SHEET 3 K 3 ASP H 220 VAL H 225 -1 O LYS H 221 N CYS H 208 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.25 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.27 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.22 SSBOND 4 CYS H 142 CYS H 208 1555 1555 2.25 LINK C ACE P 670 N ASN P 671 1555 1555 1.33 LINK C ASN P 677 N DIV P 678 1555 1555 1.33 LINK C DIV P 678 N LEU P 679 1555 1555 1.47 LINK CG1 DIV P 678 CE MK8 P 681 1555 1555 1.51 LINK C TRP P 680 N MK8 P 681 1555 1555 1.49 LINK C MK8 P 681 N ILE P 682 1555 1555 1.49 CISPEP 1 SER L 7 PRO L 8 0 -0.73 CISPEP 2 TYR L 140 PRO L 141 0 -0.29 CISPEP 3 ALA L 184 ASP L 185 0 18.28 CISPEP 4 GLU L 213 CYS L 214 0 4.68 CISPEP 5 GLY H 100A TRP H 100B 0 2.64 CISPEP 6 PHE H 148 PRO H 149 0 -1.40 CISPEP 7 GLU H 150 PRO H 151 0 -3.29 SITE 1 AC1 7 ASN P 674 ILE P 675 THR P 676 ASN P 677 SITE 2 AC1 7 LEU P 679 MK8 P 681 ILE P 682 SITE 1 AC2 6 THR H 133 SER H 134 VAL L 115 PHE L 116 SITE 2 AC2 6 LYS L 207 HOH L 412 SITE 1 AC3 3 SER H 28 PHE H 29 SER H 30 SITE 1 AC4 4 GLN H 39 ALA H 40 PRO H 41 GLY H 42 CRYST1 226.107 226.107 41.824 90.00 90.00 120.00 P 61 2 2 12 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 0.004423 0.002553 0.000000 0.00000 SCALE2 0.000000 0.005107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023910 0.00000