HEADER VIRAL PROTEIN 01-FEB-07 2JNR TITLE DISCOVERY AND OPTIMIZATION OF A NATURAL HIV-1 ENTRY INHIBITOR TITLE 2 TARGETING THE GP41 FUSION PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIR165; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ENV POLYPROTEIN; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: FP1-23; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: VIR-165 IS A MODIFIED FORM OF THE VIRUS-INHIBITORY SOURCE 6 PEPTIDE (VIRIP) WHICH NATURALLY OCCURS IN HUMAN PLASMA.; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS PEPTIDE COMPLEX, VIRAL PROTEIN EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR J.MUNCH,L.STANDKER,K.ADERMANN,A.SCHULZ,S.POHLMANN,C.CHAIPAN,T.BIET, AUTHOR 2 T.PETERS,B.MEYER,D.WILHELM,H.LU,W.JING,S.JIANG,W.FORSSMANN, AUTHOR 3 F.KIRCHHOFF REVDAT 4 20-DEC-23 2JNR 1 REMARK REVDAT 3 20-OCT-21 2JNR 1 SOURCE REMARK SEQADV REVDAT 2 24-FEB-09 2JNR 1 VERSN REVDAT 1 08-MAY-07 2JNR 0 JRNL AUTH J.MUNCH,L.STANDKER,K.ADERMANN,A.SCHULZ,M.SCHINDLER, JRNL AUTH 2 R.CHINNADURAI,S.POHLMANN,C.CHAIPAN,T.BIET,T.PETERS,B.MEYER, JRNL AUTH 3 D.WILHELM,H.LU,W.JING,S.JIANG,W.G.FORSSMANN,F.KIRCHHOFF JRNL TITL DISCOVERY AND OPTIMIZATION OF A NATURAL HIV-1 ENTRY JRNL TITL 2 INHIBITOR TARGETING THE GP41 FUSION PEPTIDE. JRNL REF CELL(CAMBRIDGE,MASS.) V. 129 263 2007 JRNL REFN ISSN 0092-8674 JRNL PMID 17448989 JRNL DOI 10.1016/J.CELL.2007.02.042 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SYBYL REMARK 3 AUTHORS : TRIPOS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JNR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000100063. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.7 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.75 MM VIR165, 0.75 MM FP1-23, REMARK 210 3%DMSO ADDED, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 500 MHZ; 250 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DPX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: DIMERIC 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 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 GLU A 2 CD GLU A 2 OE1 0.124 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 PHE A 14 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 VAL A 19 CB - CA - C ANGL. DEV. = -13.0 DEGREES REMARK 500 PHE B 108 CG - CD2 - CE2 ANGL. DEV. = 8.4 DEGREES REMARK 500 PHE B 108 CZ - CE2 - CD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 LEU B 109 CA - C - N ANGL. DEV. = 12.2 DEGREES REMARK 500 PHE B 111 CB - CG - CD2 ANGL. DEV. = -4.4 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 4 110.84 -160.70 REMARK 500 PRO A 5 34.56 -83.87 REMARK 500 CYS A 6 -92.15 -168.27 REMARK 500 SER A 7 -47.27 93.54 REMARK 500 ILE A 8 -82.20 -95.00 REMARK 500 PRO A 10 94.80 -62.45 REMARK 500 PHE A 12 59.66 -148.81 REMARK 500 ALA A 13 -46.54 91.12 REMARK 500 PHE A 14 39.19 -150.88 REMARK 500 ASN A 15 -65.53 -99.11 REMARK 500 LYS A 16 71.48 44.59 REMARK 500 PHE A 18 82.92 -156.33 REMARK 500 LEU B 107 48.37 -87.13 REMARK 500 PHE B 108 91.35 13.77 REMARK 500 LEU B 109 -35.80 71.52 REMARK 500 ALA B 114 40.91 -159.17 REMARK 500 ALA B 115 -43.32 -166.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE A 14 0.08 SIDE CHAIN REMARK 500 PHE A 18 0.09 SIDE CHAIN REMARK 500 PHE B 108 0.08 SIDE CHAIN REMARK 500 PHE B 111 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHOR STATES THAT VIR-165 IS A MODIFIED FORM OF REMARK 999 VIRUS-INHIBITORY PEPTIDE, VIRIP WHICH CORRESPONDS EXACTLY REMARK 999 TO RESIDUES 353-372 OF HUMAN ALPHA1-ANTITRYPSIN (UNP REMARK 999 ENTRY P01009). VIR-165 (LEAIPCSIPPCFAFNKPFVF) DIFFERS REMARK 999 FROM VIRIP (LEAIPMSIPPEVKFNKPFVF) BY THREE AMINO ACID REMARK 999 CHANGES THAT ENHANCE ITS ABILITY TO INHIBIT INFECTION BY REMARK 999 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1). DBREF 2JNR B 101 123 UNP Q72502 Q72502_9HIV1 510 532 DBREF 2JNR A 1 20 PDB 2JNR 2JNR 1 20 SEQADV 2JNR ARG B 122 UNP Q72502 ALA 531 ENGINEERED MUTATION SEQRES 1 A 20 LEU GLU ALA ILE PRO CYS SER ILE PRO PRO CYS PHE ALA SEQRES 2 A 20 PHE ASN LYS PRO PHE VAL PHE SEQRES 1 B 23 ALA VAL GLY ILE GLY ALA LEU PHE LEU GLY PHE LEU GLY SEQRES 2 B 23 ALA ALA GLY SER THR MET GLY ALA ARG SER SSBOND 1 CYS A 6 CYS A 11 1555 1555 2.03 CISPEP 1 PHE A 18 VAL A 19 0 -0.80 CISPEP 2 GLY B 113 ALA B 114 0 16.87 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000