10 20 30 40 50 60 70 80 1ROI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HISTOCOMPATIBILITY ANTIGEN 19-JUL-94 1ROI
TITLE MOLECULAR DYNAMICS SIMULATION OF MHC-PEPTIDE COMPLEXES AS A TITLE 2 TOOL FOR PREDICTING POTENTIAL TCELL EPITOPES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-B*2705); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE:; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 MOL_ID: 2
KEYWDS HISTOCOMPATIBILITY ANTIGEN
EXPDTA THEORETICAL MODEL
AUTHOR D.ROGNAN,L.SCAPOZZA,G.FOLKERS,A.DASER
REVDAT 1 30-SEP-94 1ROI 0
JRNL AUTH D.ROGNAN,L.SCAPOZZA,G.FOLKERS,A.DASER JRNL TITL MOLECULAR DYNAMICS SIMULATION OF MHC-PEPTIDE JRNL TITL 2 COMPLEXES AS A TOOL FOR PREDICTING POTENTIAL T JRNL TITL 3 CELL EPITOPES. JRNL REF BIOCHEMISTRY V. 33 11476 1994 JRNL REFN ASTM BICHAW US ISSN 0006-2960
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.DASER,H.URLAUB,P.HENKLEIN REMARK 1 TITL HLA-B27 BINDING PEPTIDES DERIVED FROM THE 57 KD REMARK 1 TITL 2 HEAT SHOCK PROTEIN OF CHLAMYDIA TRACHOMATIS: NOVEL REMARK 1 TITL 3 INSIGHTS INTO THE PEPTIDE BINDING RULES REMARK 1 REF MOL.IMMUNOL. V. 31 331 1994 REMARK 1 REFN ASTM MOIMD5 UK ISSN 0161-5890 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.R.MADDEN,J.C.GORGA,J.L.STROMINGER,D.C.WILEY REMARK 1 TITL THE THREE-DIMENSIONAL STRUCTURE OF HLA-B27 AT 2.1 REMARK 1 TITL 2 ANGSTROMS RESOLUTION SUGGESTS A GENERAL MECHANISM REMARK 1 TITL 3 FOR TIGHT PEPTIDE BINDING TO MHC REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 70 1035 1992 REMARK 1 REFN ASTM CELLB5 US ISSN 0092-8674
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: NULL
REMARK 4 REMARK 4 1ROI COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 5 REMARK 5 THE STRUCTURE REPRESENTS A THEORETICAL MODEL, OBTAINED REMARK 5 AFTER 150 PS MOLECULAR DYNAMICS (MD) SIMULATION OF THE REMARK 5 COMPLEX BETWEEN THE ANTIGEN-BINDING DOMAIN (GLY A 1 - THR REMARK 5 A 182) OF HLA-B*2705 AND NONAPEPTIDE RRKAMFEDI. IT SHOULD REMARK 5 BE CONSIDERED ONLY AS A CRUDE MOLECULAR MODEL USED FOR REMARK 5 STRUCTURE-ACTIVITY RELATIONSHIPS AND DRUG DESIGN PURPOSES.
REMARK 6 REMARK 6 THE ATOMIC COORDINATES PRESENTED HERE CORRESPOND TO THE REMARK 6 ENERGY-MINIMIZED STRUCTURE OF THE MD TIME-AVERAGED REMARK 6 CONFORMATION. BOTH ENERGY MINIMIZATION AND MOLECULAR REMARK 6 DYNAMICS SIMULATIONS OF THE COMPLEX WERE PERFORMED IN A REMARK 6 WATER SHELL (SEE JRNL, FOR DETAILS) USING THE AMBER 4.0 REMARK 6 SUITE OF PROGRAMS (D.A. PEARLMAN, D.A. CASE, J.C. REMARK 6 CALDWELL, G.L. SEIBEL, U.C. SINGH, P. WEINER AND P.A. REMARK 6 KOLLMAN, 1991, AMBER 4.0, UNIVERSITY OF CALIFORNIA, SAN REMARK 6 FRANCISCO).
REMARK 7 REMARK 7 THE ANTIGEN BINDING DOMAIN OF HLA-B*2705 IS IDENTIFIED AS REMARK 7 CHAIN A. THE BACTERIAL PEPTIDE IS IDENTIFIED AS CHAIN B. REMARK 7 THE C-TERMINAL AMINO ACID OF THE ANTIGEN BINDING DOMAIN REMARK 7 (THR A 182) WAS PROTECTED BY A N-METHYL GROUP (NME A 183).
REMARK 8 REMARK 8 BELOW ARE THE COORDINATES FOR LONE PAIRS OF ELECTRONS REMARK 8 REPORTED IN THIS MODEL ENTRY. THEY ARE PRESENTED EXACTLY REMARK 8 AS THEY APPEARED IN THE RAW DATA FILE SENT TO THE REMARK 8 PROTEIN DATA BANK BY THE DEPOSITOR. REMARK 8 REMARK 8 ATOM 43 LP1 MET A 5 -8.337 -5.316 1.308 REMARK 8 ATOM 44 LP2 MET A 5 -8.597 -4.195 0.629 REMARK 8 ATOM 678 LP1 CYS A 67 -2.869 6.663 0.260 REMARK 8 ATOM 679 LP2 CYS A 67 -2.600 5.351 0.251 REMARK 8 ATOM 1004 LP1 MET A 98 -0.237 -5.574 -3.070 REMARK 8 ATOM 1005 LP2 MET A 98 -0.938 -5.842 -4.179 REMARK 8 ATOM 1032 LP1 CYS A 101 -6.749 -10.503 2.391 REMARK 8 ATOM 1033 LP2 CYS A 101 -6.690 -10.134 3.676 REMARK 8 ATOM 1647 LP1 CYS A 164 -7.527 -8.209 2.534 REMARK 8 ATOM 1648 LP2 CYS A 164 -6.241 -8.173 2.156 REMARK 8 ATOM 1919 LP1 MET B 5 4.873 5.417 7.132 REMARK 8 ATOM 1920 LP2 MET B 5 4.462 6.683 7.232
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 ASP A 29 -82.96 59.68 REMARK 500 ARG A 151 125.43 81.00
DBREF 1ROI A 1 182 UNP P10318 1B18_HUMAN 25 206
SEQRES 1 A 183 GLY SER HIS SER MET ARG TYR PHE HIS THR SER VAL SER SEQRES 2 A 183 ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE THR VAL GLY SEQRES 3 A 183 TYR VAL ASP ASP THR LEU PHE VAL ARG PHE ASP SER ASP SEQRES 4 A 183 ALA ALA SER PRO ARG GLU GLU PRO ARG ALA PRO TRP ILE SEQRES 5 A 183 GLU GLN GLU GLY PRO GLU TYR TRP ASP ARG GLU THR GLN SEQRES 6 A 183 ILE CYS LYS ALA LYS ALA GLN THR ASP ARG GLU ASP LEU SEQRES 7 A 183 ARG THR LEU LEU ARG TYR TYR ASN GLN SER GLU ALA GLY SEQRES 8 A 183 SER HIS THR LEU GLN ASN MET TYR GLY CYS ASP VAL GLY SEQRES 9 A 183 PRO ASP GLY ARG LEU LEU ARG GLY TYR HIS GLN ASP ALA SEQRES 10 A 183 TYR ASP GLY LYS ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 A 183 SER SER TRP THR ALA ALA ASP THR ALA ALA GLN ILE THR SEQRES 12 A 183 GLN ARG LYS TRP GLU ALA ALA ARG VAL ALA GLU GLN LEU SEQRES 13 A 183 ARG ALA TYR LEU GLU GLY GLU CYS VAL GLU TRP LEU ARG SEQRES 14 A 183 ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG ALA SEQRES 15 A 183 NME SEQRES 1 B 9 ARG ARG LYS ALA MET PHE GLU ASP ILE
MODRES 1ROI NME A 183 METHYLAMINE
HET NME A 183 3
HETNAM NME METHYLAMINE
FORMUL 1 NME C H5 N
HELIX 1 H1 PRO A 50 ILE A 52 5 3 HELIX 2 H2 PRO A 57 TYR A 85 1 29 HELIX 3 H3 THR A 138 ALA A 150 1 13 HELIX 4 H4 VAL A 152 GLU A 163 1 12 HELIX 5 H5 VAL A 165 ASN A 174 1 10
SHEET 1 A 7 GLU A 46 PRO A 47 0 SHEET 2 A 7 THR A 31 ASP A 37 -1 SHEET 3 A 7 ILE A 23 VAL A 28 -1 SHEET 4 A 7 HIS A 3 SER A 13 -1 SHEET 5 A 7 THR A 94 VAL A 103 -1 SHEET 6 A 7 LEU A 109 ASP A 116 -1 SHEET 7 A 7 ILE A 124 ALA A 125 -1
SSBOND 1 CYS A 101 CYS A 164
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