10 20 30 40 50 60 70 80 1N2P - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER MEMBRANE PROTEIN 24-OCT-02 1N2P
TITLE IN SILICO-MODELLED MYELIN PROTEIN ZERO
COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELIN PROTEIN ZERO; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CHARCOT-MARIE-TOOTH NEUROPATHY 1B
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN
KEYWDS MYELIN PROTEIN ZERO, CHARCOT-MARIE-TOOTH NEUROPATHY 1B, KEYWDS 2 MODELER, HOMOLOGY MODELLING, NUCLEIC ACID
EXPDTA THEORETICAL MODEL
AUTHOR S.C.MALLENA,J.A.R.P.SARMA,R.STRAUSBERG
REVDAT 1 06-NOV-02 1N2P 0
JRNL AUTH S.C.MALLENA,J.A.R.P.SARMA,R.STRAUSBERG JRNL TITL SEQUENCE FROM NUCLEIC ACID JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MODELER REMARK 3 AUTHORS : SALI,BLUNDELL,FISER,SANCHEZ,MARTI-RENOM, REMARK 3 YERKOVICH,BADRETDINOV,MELO,OVERINGTON,FEYFANT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1N2P COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-OCT-2002. REMARK 100 THE RCSB ID CODE IS RCSB017443.
REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: MODELER IS AN AUTOMATED HOMOLOGY MODELING SCHEME REMARK 220 DESIGNED TO FIND THE MOST PROBABLE THREE DIMENSIONAL REMARK 220 STRUCTURE OF A PROTEIN, GIVEN ITS AMINO ACID SEQUENCE REMARK 220 AND ITS ALIGNMENT WITH RELATED STRUCTURES. IT DERIVES 3D REMARK 220 PROTEIN MODELS WITHOUT THE TIME CONSUMING SEPARATE REMARK 220 STAGES OF CORE REGION IDENTIFICATION AND LOOP REGION REMARK 220 BUILDING OR SEARCHING THAT ARE INHERENT TO MANUAL REMARK 220 HOMOLOGY MODELING SCHEMES. THE RELATED OR REFERENCE REMARK 220 PROTEIN STRUCTURES ARE USED TO DERIVE SPATIAL RESTRAINTS REMARK 220 EXPRESSED AS PROBABILITY DENSITY FUNCTIONS (PDFS) FOR REMARK 220 EACH OF THE RESTRAINED FEATURES OF THE MODEL. AS AN REMARK 220 EXAMPLE, THE MAIN CHAIN CONFORMATION OF A GIVEN RESIDUE REMARK 220 IN THE MODEL WILL BE DESCRIBED BY RESTRAINTS THAT DEPEND REMARK 220 UPON THE RESIDUE TYPE, THE MAIN CHAIN CONFORMATION OF REMARK 220 EQUIVALENT RESIDUES IN THE REFERENCE PROTEINS AND THE REMARK 220 LOCAL SEQUENCE SIMILARITY. THE PROBABILITY DISTRIBUTION REMARK 220 FUNCTIONS THAT ARE USED IN RESTRAINING THE MODEL REMARK 220 STRUCTURE ARE DERIVED FROM CORRELATIONS BETWEEN REMARK 220 STRUCTURAL FEATURES IN A DATABASE OF FAMILIES OF REMARK 220 HOMOLOGOUS PROTEINS ALIGNED ON THE BASIS OF THEIR 3D REMARK 220 STRUCTURE. THESE FUNCTIONS ARE USED TO RESTRAIN C-C REMARK 220 DISTANCES, MAIN CHAIN N-O DISTANCES, MAIN CHAIN AND SIDE REMARK 220 CHAIN DIHEDRAL ANGLES, ETC. THE INDIVIDUAL RESTRAINTS REMARK 220 ARE ASSEMBLED INTO A SINGLE MOLECULAR PROBABILITY REMARK 220 DENSITY FUNCTION (MPDF). THE THREE DIMENSIONAL PROTEIN REMARK 220 MODEL IS THEN OBTAINED BY AN OPTIMIZATION OF THIS MPDF. REMARK 220 THE OPTIMIZATION PROCEDURE ITSELF CONSISTS OF A VARIABLE REMARK 220 TARGET FUNCTION METHOD (BRAUN AND GO, 1985) WITH REMARK 220 CONJUGATE GRADIENT MINIMIZATION SCHEME FOLLOWED BY AN REMARK 220 OPTIONAL RESTRAINED SIMULATED ANNEALING MOLECULAR REMARK 220 DYNAMICS SCHEME.
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 GLU A 158 130.27 93.83
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NEU RELATED DB: PDB REMARK 900 1NEU CONTAINS MYELIN MEMBRANE ADHESION MOLECULE P0
DBREF 1N2P A 1 258 GB 13676320 AAH06491 1 258
SEQRES 1 A 258 MET LEU ARG ALA PRO ALA PRO ALA PRO ALA MET ALA PRO SEQRES 2 A 258 GLY ALA PRO SER SER SER PRO SER PRO ILE LEU ALA VAL SEQRES 3 A 258 LEU LEU PHE SER SER LEU VAL LEU SER PRO ALA GLN ALA SEQRES 4 A 258 ILE VAL VAL TYR THR ASP ARG GLU VAL HIS GLY ALA VAL SEQRES 5 A 258 GLY SER ARG VAL THR LEU HIS CYS SER PHE TRP SER SER SEQRES 6 A 258 GLU TRP VAL SER ASP ASP ILE SER PHE THR TRP ARG TYR SEQRES 7 A 258 GLN PRO GLU GLY GLY ARG ASP ALA ILE SER ILE PHE HIS SEQRES 8 A 258 TYR ALA LYS GLY GLN PRO TYR ILE ASP GLU VAL GLY THR SEQRES 9 A 258 PHE LYS GLU ARG ILE GLN TRP VAL GLY ASP PRO ARG TRP SEQRES 10 A 258 LYS ASP GLY SER ILE VAL ILE HIS ASN LEU ASP TYR SER SEQRES 11 A 258 ASP ASN GLY THR PHE THR CYS ASP VAL LYS ASN PRO PRO SEQRES 12 A 258 ASP ILE VAL GLY LYS THR SER GLN VAL THR LEU TYR VAL SEQRES 13 A 258 PHE GLU LYS VAL PRO THR ARG TYR GLY VAL VAL LEU GLY SEQRES 14 A 258 ALA VAL ILE GLY GLY VAL LEU GLY VAL VAL LEU LEU LEU SEQRES 15 A 258 LEU LEU LEU PHE TYR VAL VAL ARG TYR CYS TRP LEU ARG SEQRES 16 A 258 ARG GLN ALA ALA LEU GLN ARG ARG LEU SER ALA MET GLU SEQRES 17 A 258 LYS GLY LYS LEU HIS LYS PRO GLY LYS ASP ALA SER LYS SEQRES 18 A 258 ARG GLY ARG GLN THR PRO VAL LEU TYR ALA MET LEU ASP SEQRES 19 A 258 HIS SER ARG SER THR LYS ALA VAL SER GLU LYS LYS ALA SEQRES 20 A 258 LYS GLY LEU GLY GLU SER ARG LYS ASP LYS LYS
HELIX 1 1 ASP A 128 ASP A 131 5 4
SHEET 1 A 2 VAL A 41 TYR A 43 0 SHEET 2 A 2 SER A 61 TRP A 63 -1 O SER A 61 N TYR A 43 SHEET 1 B 6 GLU A 47 ALA A 51 0 SHEET 2 B 6 LYS A 148 PHE A 157 1 O THR A 153 N VAL A 48 SHEET 3 B 6 GLY A 133 LYS A 140 -1 N GLY A 133 O LEU A 154 SHEET 4 B 6 SER A 73 PRO A 80 -1 N SER A 73 O LYS A 140 SHEET 5 B 6 ILE A 87 ALA A 93 -1 O ILE A 87 N TYR A 78 SHEET 6 B 6 GLN A 96 ILE A 99 -1 O TYR A 98 N HIS A 91 SHEET 1 C 3 VAL A 56 LEU A 58 0 SHEET 2 C 3 ILE A 122 ILE A 124 -1 O ILE A 122 N LEU A 58 SHEET 3 C 3 ILE A 109 TRP A 111 -1 N GLN A 110 O VAL A 123
SSBOND 1 CYS A 60 CYS A 137
CISPEP 1 ASN A 141 PRO A 142 0 -12.46
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