HEADER IMMUNE SYSTEM 26-OCT-99 1QNZ TITLE NMR STRUCTURE OF THE 0.5B ANTI-HIV ANTIBODY COMPLEX WITH THE GP120 V3 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 0.5B ANTIBODY (HEAVY CHAIN); COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: FV; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 0.5B ANTIBODY (LIGHT CHAIN); COMPND 8 CHAIN: L; COMPND 9 FRAGMENT: FV; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: GP120; COMPND 13 CHAIN: P; COMPND 14 FRAGMENT: V3 PEPTIDE; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 9 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 16 ORGANISM_TAXID: 11676 KEYWDS ANTIBODY, V3 PEPTIDE, BINDING SITE, IMMUNE SYSTEM EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR V.TUGARINOV,A.ZVI,R.LEVY,Y.HAYEK,S.MATSUSHITA,J.ANGLISTER REVDAT 6 17-JAN-18 1QNZ 1 JRNL REVDAT 5 07-AUG-13 1QNZ 1 HEADER SOURCE KEYWDS REMARK REVDAT 5 2 1 VERSN DBREF SEQADV REVDAT 4 24-FEB-09 1QNZ 1 VERSN REVDAT 3 05-OCT-01 1QNZ 1 DBREF SEQADV ATOM REVDAT 2 28-SEP-01 1QNZ 1 DBREF REVDAT 1 03-JUN-00 1QNZ 0 JRNL AUTH V.TUGARINOV,A.ZVI,R.LEVY,Y.HAYEK,S.MATSUSHITA,J.ANGLISTER JRNL TITL NMR STRUCTURE OF AN ANTI-GP120 ANTIBODY COMPLEX WITH A V3 JRNL TITL 2 PEPTIDE REVEALS A SURFACE IMPORTANT FOR CO-RECEPTOR BINDING JRNL REF STRUCTURE V. 8 385 2000 JRNL REFN ISSN 0969-2126 JRNL PMID 10801487 JRNL DOI 10.1016/S0969-2126(00)00119-2 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE OF THE COMPLEX WAS REMARK 3 DETERMINED ALLOWING THE ANTIBODY CDR RESIDUES AND THE COMPLEXED REMARK 3 V3 PEPTIDE RESIDUES TO MOVE, WHILE THE ANTIBODY FRAMEWORK WAS REMARK 3 HELD FIXED DURING REFINEMENT AND MODELED AS DESCRIBED PREVIOUSLY REMARK 4 REMARK 4 1QNZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1290004315. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305 REMARK 210 PH : 7.15 REMARK 210 IONIC STRENGTH : 10 MM SODIUM PHOSPHATE BUFFER REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, NMRVIEW, XPLOR 3.8 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE OF THE COMPLEX WAS DETERMINED BY ALLOWING REMARK 210 THE CDRS OF THE 0.5B ANTIBODY AND THE V3 PEPTIDE RESIDUES TO REMARK 210 MOVE WHILE THE FRAMEWORK OF THE ANTIBODY WAS MODELED AS REMARK 210 DESCRIBED. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, 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 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 ALA H 121 76.14 -100.78 REMARK 500 PHE H 141 -76.07 72.12 REMARK 500 HIS H 153 -146.45 60.42 REMARK 500 ARG H 197 55.51 38.44 REMARK 500 ASP H 201 37.00 -88.85 REMARK 500 ALA H 215 30.99 -92.73 REMARK 500 TYR H 216 -51.73 -121.63 REMARK 500 GLN H 223 33.48 -86.96 REMARK 500 PRO L 8 106.39 -35.29 REMARK 500 TYR L 31 -165.89 -124.26 REMARK 500 ASP L 32 88.68 -58.93 REMARK 500 TYR L 36 74.69 -107.59 REMARK 500 GLN L 41 77.31 -117.13 REMARK 500 PRO L 44 99.33 -53.21 REMARK 500 PRO L 48 109.71 -59.69 REMARK 500 ALA L 55 -65.14 82.29 REMARK 500 SER L 60 100.14 -52.27 REMARK 500 ALA L 64 39.92 -86.44 REMARK 500 PHE L 66 79.80 -100.20 REMARK 500 ARG L 72 -82.51 68.65 REMARK 500 ASP L 86 32.05 -90.54 REMARK 500 LYS L 107 93.80 -67.47 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QNZ L 1 111 UNP P01665 KV3AD_MOUSE 1 111 DBREF 1QNZ H 113 231 PDB 1QNZ 1QNZ 113 231 DBREF 1QNZ P 232 249 UNP Q79416 Q79416_9HIV1 9 26 SEQADV 1QNZ ARG L 72 UNP P01665 GLY 72 CONFLICT SEQADV 1QNZ ARG L 112 UNP P01665 EXPRESSION TAG SEQADV 1QNZ SER H 137 GB 254221 PHE 25 CONFLICT SEQRES 1 H 119 GLN VAL GLN LEU GLN GLN SER GLY ALA GLU LEU VAL LYS SEQRES 2 H 119 PRO GLY ALA SER VAL LYS MET SER CYS LYS ALA SER GLY SEQRES 3 H 119 TYR THR PHE THR THR TYR PRO ILE GLU TRP MET LYS GLN SEQRES 4 H 119 ASN HIS GLY LYS SER LEU GLU TRP ILE GLY ASN PHE HIS SEQRES 5 H 119 PRO TYR SER ASP ASP THR ASN TYR ASN GLU LYS PHE LYS SEQRES 6 H 119 GLY LYS ALA LYS LEU THR VAL GLU LYS SER SER SER THR SEQRES 7 H 119 VAL TYR LEU GLU PHE SER ARG LEU THR SER ASP ASP SER SEQRES 8 H 119 ALA VAL TYR TYR CYS ALA ILE HIS TYR GLY SER ALA TYR SEQRES 9 H 119 ALA MET ASP TYR TRP GLY GLN GLY THR SER VAL THR VAL SEQRES 10 H 119 SER SER SEQRES 1 L 112 ASP ILE VAL LEU THR GLN SER PRO ALA SER LEU ALA VAL SEQRES 2 L 112 SER LEU GLY GLN ARG ALA THR ILE SER CYS LYS ALA SER SEQRES 3 L 112 GLN SER VAL ASP TYR ASP GLY ASP SER TYR MET ASN TRP SEQRES 4 L 112 TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU LEU ILE SEQRES 5 L 112 TYR ALA ALA SER ASN LEU GLU SER GLY ILE PRO ALA ARG SEQRES 6 L 112 PHE SER GLY SER GLY SER ARG THR ASP PHE THR LEU ASN SEQRES 7 L 112 ILE HIS PRO VAL GLU GLU GLU ASP ALA ALA THR TYR TYR SEQRES 8 L 112 CYS GLN GLN SER ASN GLU ASP PRO PHE THR PHE GLY SER SEQRES 9 L 112 GLY THR LYS LEU GLU ILE LYS ARG SEQRES 1 P 18 ARG LYS SER ILE ARG ILE GLN ARG GLY PRO GLY ARG ALA SEQRES 2 P 18 PHE VAL THR ILE GLY HELIX 1 1 THR H 199 ASP H 202 5 4 HELIX 2 2 GLU L 83 ALA L 87 5 5 SHEET 1 A 4 LEU L 4 GLN L 6 0 SHEET 2 A 4 ALA L 19 ALA L 25 -1 N LYS L 24 O THR L 5 SHEET 3 A 4 ASP L 74 ILE L 79 -1 N ILE L 79 O ALA L 19 SHEET 4 A 4 PHE L 66 GLY L 68 -1 N SER L 67 O ASN L 78 SHEET 1 B 2 SER L 10 SER L 14 0 SHEET 2 B 2 LYS L 107 LYS L 111 1 N LYS L 107 O LEU L 11 SHEET 1 C 3 ALA L 88 GLN L 94 0 SHEET 2 C 3 MET L 37 LYS L 43 -1 N GLN L 42 O THR L 89 SHEET 3 C 3 LYS L 49 ILE L 52 -1 N ILE L 52 O TRP L 39 SHEET 1 D 4 GLN H 115 SER H 119 0 SHEET 2 D 4 VAL H 130 SER H 137 -1 N SER H 137 O GLN H 115 SHEET 3 D 4 THR H 190 PHE H 195 -1 N PHE H 195 O VAL H 130 SHEET 4 D 4 ALA H 180 THR H 183 -1 N THR H 183 O TYR H 192 SHEET 1 E 5 THR H 225 VAL H 227 0 SHEET 2 E 5 ALA H 204 ILE H 210 -1 N TYR H 206 O THR H 225 SHEET 3 E 5 ILE H 146 ASN H 152 -1 N GLN H 151 O VAL H 205 SHEET 4 E 5 GLU H 158 HIS H 164 -1 N PHE H 163 O ILE H 146 SHEET 5 E 5 ASP H 169 TYR H 172 -1 N ASN H 171 O ASN H 162 SHEET 1 F 2 SER P 234 ARG P 236 0 SHEET 2 F 2 PHE P 245 THR P 247 -1 N VAL P 246 O ILE P 235 SSBOND 1 CYS H 134 CYS H 208 1555 1555 2.03 SSBOND 2 CYS L 23 CYS L 92 1555 1555 2.03 CISPEP 1 ASP L 98 PRO L 99 0 -0.07 CISPEP 2 GLY P 240 PRO P 241 0 -0.05 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 MASTER 109 0 0 2 20 0 0 6 0 0 0 21 END