HEADER IMMUNE SYSTEM 01-NOV-13 4NGH 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 AND A TETHERED PHOSPHATE MOIETY. 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: THIS SEQUENCE INCLUDES A MODIFIED FRAGMENT OF THE HIV SOURCE 16 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 4NGH 1 REMARK REVDAT 3 20-SEP-23 4NGH 1 REMARK LINK REVDAT 2 24-DEC-14 4NGH 1 JRNL REVDAT 1 03-DEC-14 4NGH 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. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 2.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18584 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 930 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 49.0490 - 5.1251 1.00 2709 144 0.1836 0.2463 REMARK 3 2 5.1251 - 4.0686 1.00 2555 134 0.1249 0.1624 REMARK 3 3 4.0686 - 3.5544 1.00 2490 131 0.1554 0.1902 REMARK 3 4 3.5544 - 3.2295 1.00 2496 132 0.1731 0.2157 REMARK 3 5 3.2295 - 2.9981 1.00 2481 129 0.1871 0.2644 REMARK 3 6 2.9981 - 2.8213 1.00 2444 129 0.2214 0.3062 REMARK 3 7 2.8213 - 2.6801 1.00 2479 131 0.2430 0.3334 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 : 0.86 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 49.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.790 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.39910 REMARK 3 B22 (A**2) : -5.39910 REMARK 3 B33 (A**2) : 10.79830 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 : 0.010 3592 REMARK 3 ANGLE : 1.349 4888 REMARK 3 CHIRALITY : 0.082 546 REMARK 3 PLANARITY : 0.006 626 REMARK 3 DIHEDRAL : 15.682 1278 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): -67.0131 77.7058 -0.7591 REMARK 3 T TENSOR REMARK 3 T11: 0.2722 T22: 0.2139 REMARK 3 T33: 0.4909 T12: -0.0209 REMARK 3 T13: -0.1352 T23: -0.1638 REMARK 3 L TENSOR REMARK 3 L11: 2.5505 L22: 1.8764 REMARK 3 L33: 1.5534 L12: -0.7254 REMARK 3 L13: 1.2301 L23: 0.3439 REMARK 3 S TENSOR REMARK 3 S11: -0.3496 S12: -0.2121 S13: 0.7948 REMARK 3 S21: 0.1657 S22: 0.3692 S23: -0.6685 REMARK 3 S31: -0.6327 S32: 0.2312 S33: 0.0941 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'L' AND ((RESSEQ 109:214)) REMARK 3 ORIGIN FOR THE GROUP (A): -40.9754 53.0096 5.2025 REMARK 3 T TENSOR REMARK 3 T11: 0.1908 T22: 0.3682 REMARK 3 T33: 0.3934 T12: -0.0239 REMARK 3 T13: -0.0350 T23: -0.0783 REMARK 3 L TENSOR REMARK 3 L11: 2.3495 L22: 4.5875 REMARK 3 L33: 3.1923 L12: 1.4452 REMARK 3 L13: 0.5459 L23: 1.2380 REMARK 3 S TENSOR REMARK 3 S11: -0.2782 S12: 0.0569 S13: -0.0988 REMARK 3 S21: -0.2683 S22: 0.1548 S23: -0.6040 REMARK 3 S31: 0.0452 S32: 0.3574 S33: 0.0920 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'H' AND ((RESSEQ 1:113)) REMARK 3 ORIGIN FOR THE GROUP (A): -78.2962 61.2230 -9.6088 REMARK 3 T TENSOR REMARK 3 T11: 0.2083 T22: 0.2065 REMARK 3 T33: 0.1303 T12: -0.0832 REMARK 3 T13: -0.0191 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 2.9069 L22: 5.0269 REMARK 3 L33: 1.9571 L12: -1.2767 REMARK 3 L13: 1.3104 L23: 0.1056 REMARK 3 S TENSOR REMARK 3 S11: -0.0600 S12: 0.0899 S13: 0.0109 REMARK 3 S21: -0.2891 S22: 0.2572 S23: 0.2102 REMARK 3 S31: 0.0654 S32: -0.1778 S33: -0.1014 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND ((RESSEQ 114:228)) REMARK 3 ORIGIN FOR THE GROUP (A): -53.6538 45.6979 10.3050 REMARK 3 T TENSOR REMARK 3 T11: 0.2605 T22: 0.2718 REMARK 3 T33: 0.2213 T12: -0.0509 REMARK 3 T13: -0.0059 T23: -0.0752 REMARK 3 L TENSOR REMARK 3 L11: 3.3444 L22: 2.4685 REMARK 3 L33: 3.4772 L12: 1.0260 REMARK 3 L13: 1.0979 L23: 0.5543 REMARK 3 S TENSOR REMARK 3 S11: 0.1769 S12: -0.6351 S13: 0.1206 REMARK 3 S21: 0.2511 S22: -0.2497 S23: -0.1647 REMARK 3 S31: 0.2457 S32: -0.1334 S33: 0.0333 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'P' AND ((RESSEQ 670:678)) REMARK 3 ORIGIN FOR THE GROUP (A): -91.6626 76.2445 -12.0637 REMARK 3 T TENSOR REMARK 3 T11: 0.3665 T22: 0.5147 REMARK 3 T33: 0.4277 T12: 0.0322 REMARK 3 T13: -0.1403 T23: 0.0739 REMARK 3 L TENSOR REMARK 3 L11: 2.6727 L22: 3.7256 REMARK 3 L33: 4.3097 L12: 2.7400 REMARK 3 L13: -1.8973 L23: -0.5987 REMARK 3 S TENSOR REMARK 3 S11: 0.0126 S12: 0.3067 S13: 0.2420 REMARK 3 S21: -0.3796 S22: 0.2674 S23: 0.7534 REMARK 3 S31: 0.2014 S32: -0.7812 S33: -0.1562 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 4NGH 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_1000083172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5.5 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) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18587 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 REMARK 200 RESOLUTION RANGE LOW (A) : 49.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 28.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.59700 REMARK 200 FOR SHELL : 5.600 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 (%): 61.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION:0.2 M MGCL2, 0.1 M REMARK 280 MES PH5.5, 40% PEG 400, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 14.11000 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 28.22000 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 21.16500 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 35.27500 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 7.05500 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 14.11000 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 28.22000 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 35.27500 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 21.16500 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 7.05500 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: 5630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH L 301 LIES ON A SPECIAL POSITION. 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)I(LYV)KKK IS PEPTIDE- REMARK 400 LIKE, A MEMBER OF UNKNOWN CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: STAPLED PEPTIDE (ACE)NWFNITN(DIV)LW(MK8)I(LYV)KKK 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 0.156 REMARK 500 LYV P 683 C LYS P 684 N 0.169 REMARK 500 LYS P 684 C LYS P 685 N 0.142 REMARK 500 LYS P 685 C LYS P 686 N 0.193 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 ALA L 184 N - CA - C ANGL. DEV. = -16.3 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 L 40 -69.39 -18.29 REMARK 500 ALA L 51 -44.74 71.55 REMARK 500 ASN L 152 6.30 59.25 REMARK 500 ARG L 211 106.28 -59.83 REMARK 500 VAL H 2 89.13 71.16 REMARK 500 TRP H 100B 83.02 55.64 REMARK 500 LEU H 100C 82.71 -64.24 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NHC 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. DBREF 4NGH L 1 214 PDB 4NGH 4NGH 1 214 DBREF 4NGH H 1 228 PDB 4NGH 4NGH 1 228 DBREF 4NGH P 670 686 PDB 4NGH 4NGH 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 LYV LYS LYS LYS MODRES 4NGH MK8 P 681 LEU 2-METHYL-L-NORLEUCINE HET ACE P 670 3 HET DIV P 678 7 HET MK8 P 681 9 HET LYV P 683 21 HETNAM ACE ACETYL GROUP HETNAM DIV D-ISOVALINE HETNAM MK8 2-METHYL-L-NORLEUCINE HETNAM LYV O-PHOSPHONO-L-SERYL-N-[(3S)-3-AMINO-3- HETNAM 2 LYV CARBOXYPROPYL]GLYCINAMIDE FORMUL 3 ACE C2 H4 O FORMUL 3 DIV C5 H11 N O2 FORMUL 3 MK8 C7 H15 N O2 FORMUL 3 LYV C9 H19 N4 O8 P FORMUL 4 HOH *96(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 PRO H 61 GLN H 64 5 4 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 GLY H 199 5 4 HELIX 8 8 LYS H 213 ASN H 216 5 4 HELIX 9 9 ASN P 671 PHE P 673 5 3 HELIX 10 10 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 LYS L 103 N GLN L 11 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 LYS L 103 N GLN L 11 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 LEU L 135 N PHE L 116 SHEET 3 D 4 TYR L 173 SER L 182 -1 O LEU L 181 N ALA L 130 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 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 E 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 E 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SHEET 1 F 4 GLN H 3 GLN H 6 0 SHEET 2 F 4 VAL H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 F 4 THR H 77 LEU H 82 -1 O LEU H 80 N VAL H 20 SHEET 4 F 4 ILE H 67 ASP H 72 -1 N ASP H 72 O THR H 77 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 ALA H 88 O VAL H 109 SHEET 4 G 6 LEU H 34 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 G 6 GLU H 46 ILE H 52 -1 O GLY H 49 N TRP H 36 SHEET 6 G 6 ILE H 56 TYR H 59 -1 O ASN H 58 N GLY H 50 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 ALA H 88 O VAL H 109 SHEET 4 H 4 PRO H 100F TRP H 103 -1 O ILE H 100G N GLY H 96 SHEET 1 I 4 SER H 120 LEU H 124 0 SHEET 2 I 4 THR H 137 TYR H 147 -1 O GLY H 141 N LEU H 124 SHEET 3 I 4 TYR H 185 PRO H 194 -1 O TYR H 185 N TYR H 147 SHEET 4 I 4 HIS H 172 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 HIS H 212 -1 O ASN H 209 N SER H 156 SHEET 3 K 3 THR H 217 VAL H 225 -1 O VAL H 219 N VAL H 210 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.31 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.32 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.25 SSBOND 4 CYS H 142 CYS H 208 1555 1555 2.26 LINK C ACE P 670 N ASN P 671 1555 1555 1.31 LINK C ASN P 677 N DIV P 678 1555 1555 1.34 LINK C DIV P 678 N LEU P 679 1555 1555 1.45 LINK CG1 DIV P 678 CE MK8 P 681 1555 1555 1.47 LINK C TRP P 680 N MK8 P 681 1555 1555 1.49 LINK C MK8 P 681 N ILE P 682 1555 1555 1.46 LINK C ILE P 682 N LYV P 683 1555 1555 1.43 LINK C LYV P 683 N LYS P 684 1555 1555 1.51 CISPEP 1 SER L 7 PRO L 8 0 -11.01 CISPEP 2 TYR L 140 PRO L 141 0 3.66 CISPEP 3 ALA L 184 ASP L 185 0 22.38 CISPEP 4 GLU L 213 CYS L 214 0 8.57 CISPEP 5 GLY H 99 TRP H 100 0 7.67 CISPEP 6 GLY H 100A TRP H 100B 0 4.19 CISPEP 7 PHE H 148 PRO H 149 0 -4.35 CISPEP 8 GLU H 150 PRO H 151 0 -0.84 SITE 1 AC1 8 ASN P 674 ILE P 675 THR P 676 ASN P 677 SITE 2 AC1 8 LEU P 679 TRP P 680 MK8 P 681 ILE P 682 CRYST1 226.510 226.510 42.330 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 0.004415 0.002549 0.000000 0.00000 SCALE2 0.000000 0.005098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023624 0.00000