10 20 30 40 50 60 70 80 1OBE - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER COMPLEX (IMMUNOGLOBULIN/PEPTIDE) 27-JAN-97 1OBE
TITLE IGG1 FAB FRAGMENT 3D6 COMPLEXED WITH SYNTHETIC PEPTIDE, TITLE 2 THEORETICAL MODEL
COMPND MOL_ID: 1; COMPND 2 MOLECULE: IGG1 FAB FRAGMENT 3D6; COMPND 3 CHAIN: L; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: IGG1 FAB FRAGMENT 3D6; COMPND 6 CHAIN: H; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: GP41; COMPND 9 CHAIN: P; COMPND 10 FRAGMENT: RESIDUES 605 - 617; COMPND 11 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_COMMON: HUMAN; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES
KEYWDS COMPLEX (IMMUNOGLOBULIN/PEPTIDE), COAT PROTEIN, POLYPROTEIN, KEYWDS 2 GLYCOPROTEIN
EXPDTA THEORETICAL MODEL
AUTHOR R.-D.STIGLER,J.SCHNEIDER-MERGENER
REVDAT 1 15-MAY-97 1OBE 0
JRNL AUTH R.D.STIGLER,F.RUKER,D.KATINGER,G.ELLIOTT,W.HOHNE, JRNL AUTH 2 P.HENKLEIN,J.X.HO,K.KEELING,D.C.CARTER,E.NUGEL, JRNL AUTH 3 ET AL. JRNL TITL INTERACTION BETWEEN A FAB FRAGMENT AGAINST GP41 OF JRNL TITL 2 HUMAN IMMUNODEFICIENCY VIRUS 1 AND ITS PEPTIDE JRNL TITL 3 EPITOPE: CHARACTERIZATION USING A PEPTIDE EPITOPE JRNL TITL 4 LIBRARY AND MOLECULAR MODELING JRNL REF PROTEIN ENG. V. 8 471 1995 JRNL REFN ASTM PRENE9 UK ISSN 0269-2139
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.M.HE,F.RUKER,E.CASALE,D.C.CARTER REMARK 1 TITL STRUCTURE OF A HUMAN MONOCLONAL ANTIBODY FAB REMARK 1 TITL 2 FRAGMENT AGAINST GP41 OF HUMAN IMMUNODEFICIENCY REMARK 1 TITL 3 VIRUS TYPE 1 REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 89 7154 1992 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE MODEL OF THE 3D6 FAB FRAGMENT REMARK 3 WAS BUILT USING ATOM COORDINATES OF HE ET AL. (PDB-ENTRY 1DFB) REMARK 3 . A BETA-1 TURN CONFORMATION OF THE PEPTIDE EPITOPE REMARK 3 CSGKLICTTAVPW WAS HAND-DOCKED TO THE ANTIBODY BINDING REGION; REMARK 3 THE ORIENTATION WAS SUPPORTED BY ELECTRON DENSITY MAPS. THE REMARK 3 RESULTING MODEL COMPLEX WAS SUBJECTED TO ENERGY-MINIMIZATION REMARK 3 TO A LOCAL ENERGY MINIMUM. THE SOFTWARE USED WAS CHARMM REMARK 3 (B.R.BROOKS ET AL. (1983), J.COMPUT.CHEM. 4, 187). THE REMARK 3 MINIMIZATION WAS PERFORMED INCLUDING POLAR HYDROGEN ATOMS.
REMARK 4 REMARK 4 1OBE COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 6 REMARK 6 THE LIGHT CHAIN VARIABLE REGION HAS BEEN ASSIGNED CHAIN REMARK 6 IDENTIFIER L. THE HEAVY CHAIN VARIABLE REGION HAS BEEN REMARK 6 ASSIGNED CHAIN IDENTIFIER H. THE PEPTIDE EPITOPE HAS BEEN REMARK 6 ASSIGNED CHAIN IDENTIFIER P.
REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL
REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.
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 M RES CSSEQI PSI PHI REMARK 500 SER L 30 -46.76 82.36 REMARK 500 ALA L 51 -43.38 67.73 REMARK 500 ASN L 92 -80.29 135.84 REMARK 500 ASN L 150 -78.41 69.51 REMARK 500 SER H 143 -26.47 121.73 REMARK 500 LYS P 4 -39.93 68.66 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 SER L 28 ILE L 29 144.04 REMARK 500 CYS L 88 GLN L 89 146.41 REMARK 500 ARG H 72 ASP H 73 144.57 REMARK 500 LYS H 142 SER H 143 -145.89 REMARK 500 VAL H 194 VAL H 195 148.43 REMARK 500 THR P 9 ALA P 10 -143.72
REMARK 850 REMARK 850 CORRECTION BEFORE RELEASE REMARK 850 ORIGINAL DEPOSITION REVISED PRIOR TO RELEASE REMARK 850 DATE REVISED: 26-FEB-1997 TRACKING NUMBER: T10558
REMARK 999 REMARK 999 SEQUENCE REMARK 999 1OBE P SWS P19550 1 - 588 NOT IN ATOMS LIST REMARK 999 1OBE P SWS P19550 602 - 847 NOT IN ATOMS LIST
DBREF 1OBE L 1 212 PDB 1OBE 1OBE 1 212 DBREF 1OBE H 1 229 PDB 1OBE 1OBE 1 229 DBREF 1OBE P 1 13 UNP P19550 ENV_HV1S1 589 601
SEQRES 1 L 212 ASP ILE GLN MET THR GLN SER PRO SER THR LEU SER ALA SEQRES 2 L 212 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 212 GLN SER ILE SER ARG TRP LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 212 PRO GLY LYS VAL PRO LYS LEU LEU ILE TYR LYS ALA SER SEQRES 5 L 212 SER LEU GLU SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 212 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 212 GLN PRO ASP ASP PHE ALA THR TYR TYR CYS GLN GLN TYR SEQRES 8 L 212 ASN SER TYR SER PHE GLY PRO GLY THR LYS VAL ASP ILE SEQRES 9 L 212 LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE PHE PRO SEQRES 10 L 212 PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SER VAL SEQRES 11 L 212 VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU ALA LYS SEQRES 12 L 212 VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER GLY ASN SEQRES 13 L 212 SER GLN GLU SER VAL THR GLU GLN ASP SER LYS ASP SER SEQRES 14 L 212 THR TYR SER LEU SER SER THR LEU THR LEU SER LYS ALA SEQRES 15 L 212 ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU VAL THR SEQRES 16 L 212 HIS GLN GLY LEU SER SER PRO VAL THR LYS SER PHE ASN SEQRES 17 L 212 ARG GLY GLU CYS SEQRES 1 H 229 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 229 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 229 PHE THR PHE ASN ASP TYR ALA MET HIS TRP VAL ARG GLN SEQRES 4 H 229 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER GLY ILE SER SEQRES 5 H 229 TRP ASP SER SER SER ILE GLY TYR ALA ASP SER VAL LYS SEQRES 6 H 229 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 229 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP MET SEQRES 8 H 229 ALA LEU TYR TYR CYS VAL LYS GLY ARG ASP TYR TYR ASP SEQRES 9 H 229 SER GLY GLY TYR PHE THR VAL ALA PHE ASP ILE TRP GLY SEQRES 10 H 229 GLN GLY THR MET VAL THR VAL SER SER ALA SER THR LYS SEQRES 11 H 229 GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SER SEQRES 12 H 229 THR SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS SEQRES 13 H 229 ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER SEQRES 14 H 229 GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL SEQRES 15 H 229 LEU GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL SEQRES 16 H 229 THR VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE SEQRES 17 H 229 CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP SEQRES 18 H 229 LYS LYS VAL GLU PRO LYS SER CYS SEQRES 1 P 13 CYS SER GLY LYS LEU ILE CYS THR THR ALA VAL PRO TRP
HELIX 1 1 ASP L 120 SER L 125 1 6 HELIX 2 2 LYS L 181 TYR L 184 1 4 HELIX 3 3 PHE H 29 ASP H 31 5 3 HELIX 4 4 SER H 199 SER H 201 5 3 HELIX 5 5 LYS H 214 SER H 216 5 3
SHEET 1 A 4 MET L 4 SER L 7 0 SHEET 2 A 4 VAL L 19 ALA L 25 -1 N ARG L 24 O THR L 5 SHEET 3 A 4 GLU L 70 ILE L 75 -1 N ILE L 75 O VAL L 19 SHEET 4 A 4 PHE L 62 GLY L 66 -1 N SER L 65 O THR L 72 SHEET 1 B 5 THR L 10 ALA L 13 0 SHEET 2 B 5 THR L 100 ILE L 104 1 N LYS L 101 O LEU L 11 SHEET 3 B 5 ALA L 84 GLN L 90 -1 N TYR L 86 O THR L 100 SHEET 4 B 5 LEU L 33 GLN L 38 -1 N GLN L 38 O THR L 85 SHEET 5 B 5 LYS L 45 TYR L 49 -1 N ILE L 48 O TRP L 35 SHEET 1 C 4 SER L 112 PHE L 116 0 SHEET 2 C 4 THR L 127 ASN L 135 -1 N ASN L 135 O SER L 112 SHEET 3 C 4 LEU L 173 SER L 180 -1 N LEU L 179 O ALA L 128 SHEET 4 C 4 SER L 157 VAL L 161 -1 N SER L 160 O SER L 174 SHEET 1 D 3 ALA L 142 VAL L 148 0 SHEET 2 D 3 VAL L 189 HIS L 196 -1 N THR L 195 O LYS L 143 SHEET 3 D 3 VAL L 203 ASN L 208 -1 N PHE L 207 O TYR L 190 SHEET 1 E 4 LEU H 4 SER H 7 0 SHEET 2 E 4 LEU H 18 ALA H 24 -1 N ALA H 23 O VAL H 5 SHEET 3 E 4 SER H 78 MET H 83 -1 N MET H 83 O LEU H 18 SHEET 4 E 4 THR H 69 ASP H 73 -1 N ASP H 73 O SER H 78 SHEET 1 F 4 TYR H 95 VAL H 97 0 SHEET 2 F 4 HIS H 35 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 3 F 4 LEU H 45 ILE H 51 -1 N SER H 49 O TRP H 36 SHEET 4 F 4 ILE H 58 TYR H 60 -1 N GLY H 59 O GLY H 50 SHEET 1 G 4 SER H 133 LEU H 137 0 SHEET 2 G 4 THR H 148 LYS H 156 -1 N LYS H 156 O SER H 133 SHEET 3 G 4 SER H 192 PRO H 198 -1 N VAL H 197 O ALA H 149 SHEET 4 G 4 VAL H 176 PHE H 179 -1 N PHE H 179 O SER H 192 SHEET 1 H 3 THR H 164 TRP H 167 0 SHEET 2 H 3 ILE H 208 HIS H 213 -1 N ASN H 212 O THR H 164 SHEET 3 H 3 THR H 218 LYS H 223 -1 N LYS H 222 O CYS H 209
SSBOND 1 CYS L 23 CYS L 88 SSBOND 2 CYS L 132 CYS L 192 SSBOND 3 CYS L 212 CYS H 229 SSBOND 4 CYS H 22 CYS H 96 SSBOND 5 CYS H 153 CYS H 209 SSBOND 6 CYS P 1 CYS P 7
CISPEP 1 SER L 7 PRO L 8 0 -3.37 CISPEP 2 TYR L 138 PRO L 139 0 -6.02 CISPEP 3 PHE H 159 PRO H 160 0 -6.79 CISPEP 4 GLU H 161 PRO H 162 0 -4.60
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