10 20 30 40 50 60 70 80 1ROG - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HISTOCOMPATIBILITY ANTIGEN 19-JUL-94 1ROG
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 1ROG 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 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 1ROG 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 RRIKAITLK. 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 MODEL PEPTIDE IS IDENTIFIED AS CHAIN B. THE REMARK 7 C-TERMINAL AMINO ACID OF THE ANTIGEN BINDING DOMAIN (THR A REMARK 7 182) WAS PROTECTED BY A N-METHYL GROUP (NME A 183). THREE REMARK 7 WATER MOLECULES (HOH 1 - HOH 3) BRIDGE THE BINDING OF THE REMARK 7 PEPTIDE TO THE HLA-B27 HISTOCOMPATIBILITY PROTEIN.
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 -8.392 -4.741 1.681 REMARK 8 ATOM 44 LP2 MET A 5 -7.431 -3.854 1.410 REMARK 8 ATOM 678 LP1 CYS A 67 -0.209 6.099 -0.325 REMARK 8 ATOM 679 LP2 CYS A 67 -1.361 6.378 -0.939 REMARK 8 ATOM 1004 LP1 MET A 98 0.760 -8.714 -3.656 REMARK 8 ATOM 1005 LP2 MET A 98 -0.098 -7.870 -4.239 REMARK 8 ATOM 1032 LP1 CYS A 101 -5.112 -10.260 3.207 REMARK 8 ATOM 1033 LP2 CYS A 101 -4.751 -9.652 4.342 REMARK 8 ATOM 1647 LP1 CYS A 164 -6.465 -8.246 3.395 REMARK 8 ATOM 1648 LP2 CYS A 164 -5.409 -7.930 2.629
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: 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 8 N PHE A 8 CA -0.089 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 GLU A 19 126.61 75.29 REMARK 500 ASP A 29 -71.73 60.06 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 TYR A 113 HIS A 114 137.29
DBREF 1ROG 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 ILE LYS ALA ILE THR LEU LYS
MODRES 1ROG NME A 183 METHYLAMINE
FTNOTE 1 TYR A 113 - HIS A 114 OMEGA = 137.29 PEPTIDE BOND DEVIATES FTNOTE 1 SIGNIFICANTLY FROM TRANS CONFORMATION
HET NME A 183 3
HETNAM NME METHYLAMINE
FORMUL 1 NME C H5 N FORMUL 3 HOH *3(H2 O1)
HELIX 1 H1 PRO A 57 TYR A 85 1 29 HELIX 2 H2 THR A 138 ALA A 149 1 12 HELIX 3 H3 ALA A 153 GLU A 161 1 9 HELIX 4 H4 GLU A 163 ASN A 174 1 12
SHEET 1 A 8 GLU A 46 PRO A 47 0 SHEET 2 A 8 THR A 31 ASP A 37 -1 SHEET 3 A 8 ILE A 23 VAL A 28 -1 SHEET 4 A 8 HIS A 3 VAL A 12 -1 SHEET 5 A 8 THR A 94 VAL A 103 -1 SHEET 6 A 8 LEU A 109 TYR A 118 -1 SHEET 7 A 8 LYS A 121 LEU A 126 -1 SHEET 8 A 8 TRP A 133 THR A 134 -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