1UPZ - Header Asymmetric Unit

HEADER OXIDOREDUCTASE 15-OCT-03 1UPZ

TITLE REDUCED GLUTAREDOXIN 1 SIMULATION TRAJECTORY, MODELS 71-141

COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN 1; COMPND 3 CHAIN: G; COMPND 4 SYNONYM: GRX1; COMPND 5 OTHER_DETAILS: MODEL, 350 STRUCTURES FROM 75 NS MD COMPND 6 SIMULATION. THIS ENTRY HAS 70 MODELS. THE OTHER ENTRIES COMPND 7 ARE 1UPY, 1UQ0, 1UQ1 AND 1UQ2

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 OTHER_DETAILS: INITIAL MODEL COORDINATES TAKEN FROM 1EGR

KEYWDS ELECTRON TRANSPORT, OXIDOREDUCTASE, DEOXYRIBONUCLEOTIDE KEYWDS 2 SYNTHESIS

EXPDTA THEORETICAL MODEL

AUTHOR N.FOLOPPE,L.NILSSON

REVDAT 2 19-FEB-04 1UPZ 1 JRNL REVDAT 1 06-NOV-03 1UPZ 0

JRNL AUTH N.FOLOPPE,L.NILSSON JRNL TITL THE GLUTAREDOXIN-C-P-Y-C- MOTIF; INFLUENCE OF JRNL TITL 2 PERIPHERAL RESIDUES JRNL REF STRUCTURE V. 12 289 2004 JRNL REFN ASTM STRUE6 UK ISSN 0969-2126

REMARK 1

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 1UPZ COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI ON 15-OCT-2003. REMARK 100 THE EBI ID CODE IS EBI-13718.

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 400 REMARK 400 COMPOUND THE RESULTS OF THE SIMULATION ARE SPLIT ACROSS 5 REMARK 400 PDB ENTRIES. THIS IS PART 2 OF 5 (350 MODELS ALTOGETHER). REMARK 400 THIS ENTRY CONTAINS 70 MODELS OF THE TIME COURSE MD REMARK 400 SIMULATION. THE OTHER ENTRIES ARE AS FOLLOWS: 1UPY : MODELS REMARK 400 1 - 70 1UQ0 : MODELS 141 - 210 1UQ1 : MODELS 211 - 280 1UQ2 REMARK 400 : MODELS 281 - 350 FUNCTION: THE DISULFIDE BOND FUNCTIONS REMARK 400 AS AN ELECTRON CARRIER IN THE GLUTATHIONE-DEPENDENT REMARK 400 SYNTHESIS OF DEOXYRIBONUCLEOTIDES BY T ENZYME REMARK 400 RIBONUCLEOTIDE REDUCTASE. IN ADDITION, IT IS ALSO INVOLVE REMARK 400 IN REDUCING SOME DISULFIDES IN A COUPLED SYSTEM WITH REMARK 400 GLUTATHIONE REDUCTASE.

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 71 ASP G 65 -96.25 59.54 REMARK 500 72 ASP G 65 -96.16 44.24 REMARK 500 73 ASP G 65 -103.62 61.72 REMARK 500 74 ASP G 65 -110.67 64.67 REMARK 500 75 ASP G 65 -114.12 58.15 REMARK 500 76 ASP G 65 -112.40 38.96 REMARK 500 77 ASP G 65 -94.50 57.77 REMARK 500 78 ASP G 65 -90.21 73.80 REMARK 500 79 ASP G 65 -96.59 59.63 REMARK 500 80 ASP G 65 -109.48 47.88 REMARK 500 81 ASP G 65 -110.11 55.34 REMARK 500 82 ASP G 65 -86.61 50.39 REMARK 500 83 ASP G 65 -110.65 66.24 REMARK 500 84 ASP G 65 -110.20 56.68 REMARK 500 85 ASP G 65 -115.91 54.32 REMARK 500 87 ASP G 65 -106.87 61.88 REMARK 500 88 ASP G 65 -110.15 62.51 REMARK 500 89 ASP G 65 -108.20 69.78 REMARK 500 91 ASP G 65 -101.79 50.72 REMARK 500 92 ASP G 65 -117.53 63.49 REMARK 500 93 ASP G 65 -101.95 76.20 REMARK 500 94 ASP G 65 -88.62 59.95 REMARK 500 95 ASP G 65 -119.89 61.31 REMARK 500 96 ASP G 65 -108.21 78.04 REMARK 500 97 ASP G 65 -87.06 64.95 REMARK 500 98 ASP G 65 -79.23 62.81 REMARK 500 99 ASP G 65 -89.66 54.40 REMARK 500 100 ASP G 65 -66.76 72.29 REMARK 500 101 ASP G 65 -108.74 59.73 REMARK 500 102 ASP G 65 -99.44 69.64 REMARK 500 103 ASP G 65 -100.03 69.12 REMARK 500 104 ASP G 65 -95.61 42.66 REMARK 500 105 ASP G 65 -99.32 69.31 REMARK 500 106 ASP G 65 -90.19 72.88 REMARK 500 107 ASP G 65 -111.27 68.99 REMARK 500 108 ASP G 65 -104.23 45.07 REMARK 500 110 ASP G 65 -119.53 68.62 REMARK 500 111 ASP G 65 -96.25 61.46 REMARK 500 112 ASP G 65 -112.40 59.66 REMARK 500 113 ASP G 65 -105.17 49.54 REMARK 500 114 ASP G 65 -110.79 70.37 REMARK 500 115 ASP G 65 -91.83 72.60 REMARK 500 116 ASP G 65 -100.45 59.73 REMARK 500 117 ASP G 65 -104.75 66.46 REMARK 500 118 ASP G 65 -95.27 72.04 REMARK 500 119 ASP G 65 -94.05 53.56 REMARK 500 120 ASP G 65 -98.63 54.66 REMARK 500 121 ASP G 65 -78.57 64.83 REMARK 500 122 ASP G 65 -90.68 62.54 REMARK 500 124 ASP G 65 -107.12 69.73 REMARK 500 125 ASP G 65 -95.96 43.65 REMARK 500 126 ASP G 65 -109.26 56.91 REMARK 500 127 ASP G 65 -108.56 43.20 REMARK 500 128 ASP G 65 -106.22 55.57 REMARK 500 129 ASP G 65 -98.11 45.77 REMARK 500 130 ASP G 65 -97.40 55.74 REMARK 500 131 ASP G 65 -104.37 36.81 REMARK 500 132 ASP G 65 -78.19 75.51 REMARK 500 133 ASP G 65 -102.34 62.80 REMARK 500 134 ASP G 65 -101.81 46.26 REMARK 500 135 ASP G 65 -93.62 61.34 REMARK 500 137 ASP G 65 -98.92 49.90 REMARK 500 138 ASP G 65 -98.61 53.02 REMARK 500 139 ASP G 65 -102.08 60.72 REMARK 500 140 ASP G 65 -119.80 59.07 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 VAL G 59 PRO G 60 72 -32.97 REMARK 500 PHE G 31 GLN G 32 89 148.01 REMARK 500 VAL G 56 GLU G 57 90 145.71 REMARK 500 LEU G 48 GLN G 49 95 -149.80 REMARK 500 GLU G 41 GLY G 42 100 142.79 REMARK 500 VAL G 59 PRO G 60 113 -34.35 REMARK 500 GLU G 81 ASN G 82 117 -149.12 REMARK 500 VAL G 59 PRO G 60 120 -38.49 REMARK 500 PRO G 60 GLN G 61 127 144.68 REMARK 500 GLN G 66 GLN G 67 128 -147.64 REMARK 500 GLU G 41 GLY G 42 134 147.76 REMARK 500 CYS G 11 PRO G 12 136 -148.39

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CC REMARK 800 SITE_DESCRIPTION: CYS 11 (THIOLATE) AND CYS 14 ARE REMARK 800 THE ACTIVE CYSTEINS INVOLVED IN DISULFIDE FORMATION

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EGO RELATED DB: PDB REMARK 900 GLUTAREDOXIN (OXIDIZED) (NMR, 20 STRUCTURES) REMARK 900 RELATED ID: 1EGR RELATED DB: PDB REMARK 900 GLUTAREDOXIN (REDUCED) (NMR, 20 STRUCTURES) REMARK 900 RELATED ID: 1GRX RELATED DB: PDB REMARK 900 STRUCTURE OF E. COLI GLUTAREDOXIN REMARK 900 RELATED ID: 1QFN RELATED DB: PDB REMARK 900 GLUTAREDOXIN-1-RIBONUCLEOTIDE REDUCTASE B1 REMARK 900 MIXED DISULFIDE BOND REMARK 900 RELATED ID: 1UPY RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 1 SIMULATION TRAJECTORY, REMARK 900 MODELS 1-70 REMARK 900 RELATED ID: 1UQ0 RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 1 SIMULATION TRAJECTORY, REMARK 900 MODELS 141-210 REMARK 900 RELATED ID: 1UQ1 RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 1 SIMULATION TRAJECTORY, REMARK 900 MODELS 211-280 REMARK 900 RELATED ID: 1UQ2 RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 1 SIMULATION TRAJECTORY, REMARK 900 MODELS 281-350 REMARK 900 RELATED ID: 1UQ3 RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 1 SIMULATION TRAJECTORY, REMARK 900 MODELS 1-70 REMARK 900 RELATED ID: 1UQ6 RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 1 SIMULATION TRAJECTORY, REMARK 900 MODELS 141-210 REMARK 900 RELATED ID: 1UQ7 RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 1 SIMULATION TRAJECTORY, REMARK 900 MODELS 211-280

DBREF 1UPZ G 1 85 UNP P00277 GLR1_ECOLI 1 85

SEQRES 1 G 85 MET GLN THR VAL ILE PHE GLY ARG SER GLY CYS PRO TYR SEQRES 2 G 85 CYS VAL ARG ALA LYS ASP LEU ALA GLU LYS LEU SER ASN SEQRES 3 G 85 GLU ARG ASP ASP PHE GLN TYR GLN TYR VAL ASP ILE ARG SEQRES 4 G 85 ALA GLU GLY ILE THR LYS GLU ASP LEU GLN GLN LYS ALA SEQRES 5 G 85 GLY LYS PRO VAL GLU THR VAL PRO GLN ILE PHE VAL ASP SEQRES 6 G 85 GLN GLN HIS ILE GLY GLY TYR THR ASP PHE ALA ALA TRP SEQRES 7 G 85 VAL LYS GLU ASN LEU ASP ALA

HELIX 1 1 CYS G 11 ARG G 28 1 18 HELIX 2 2 ARG G 39 ILE G 43 1 5 HELIX 3 3 THR G 44 GLN G 49 1 6 HELIX 4 4 GLY G 71 VAL G 79 1 9

SHEET 1 GA 4 GLN G 32 ASP G 37 0 SHEET 2 GA 4 GLN G 2 GLY G 7 1 O THR G 3 N GLN G 34 SHEET 3 GA 4 GLN G 61 VAL G 64 -1 O GLN G 61 N PHE G 6 SHEET 4 GA 4 GLN G 67 GLY G 70 -1 O GLN G 67 N VAL G 64

CISPEP 1 VAL G 59 PRO G 60 71 -6.81 CISPEP 2 VAL G 59 PRO G 60 73 -23.88 CISPEP 3 VAL G 59 PRO G 60 74 -19.40 CISPEP 4 VAL G 59 PRO G 60 75 1.66 CISPEP 5 VAL G 59 PRO G 60 76 -27.94 CISPEP 6 VAL G 59 PRO G 60 77 -0.43 CISPEP 7 VAL G 59 PRO G 60 78 -13.26 CISPEP 8 VAL G 59 PRO G 60 79 -12.26 CISPEP 9 VAL G 59 PRO G 60 80 -22.95 CISPEP 10 VAL G 59 PRO G 60 81 11.78 CISPEP 11 VAL G 59 PRO G 60 82 -4.38 CISPEP 12 VAL G 59 PRO G 60 83 9.67 CISPEP 13 VAL G 59 PRO G 60 84 -7.65 CISPEP 14 VAL G 59 PRO G 60 85 -13.00 CISPEP 15 VAL G 59 PRO G 60 86 7.53 CISPEP 16 VAL G 59 PRO G 60 87 -7.62 CISPEP 17 VAL G 59 PRO G 60 88 -5.14 CISPEP 18 VAL G 59 PRO G 60 89 -4.39 CISPEP 19 VAL G 59 PRO G 60 90 -7.06 CISPEP 20 VAL G 59 PRO G 60 91 -16.37 CISPEP 21 VAL G 59 PRO G 60 92 19.98 CISPEP 22 VAL G 59 PRO G 60 93 -3.32 CISPEP 23 VAL G 59 PRO G 60 94 0.61 CISPEP 24 VAL G 59 PRO G 60 95 -5.34 CISPEP 25 VAL G 59 PRO G 60 96 -3.61 CISPEP 26 VAL G 59 PRO G 60 97 21.25 CISPEP 27 VAL G 59 PRO G 60 98 0.82 CISPEP 28 VAL G 59 PRO G 60 99 -2.39 CISPEP 29 VAL G 59 PRO G 60 100 -21.49 CISPEP 30 VAL G 59 PRO G 60 101 -19.73 CISPEP 31 VAL G 59 PRO G 60 102 18.37 CISPEP 32 VAL G 59 PRO G 60 103 -17.55 CISPEP 33 VAL G 59 PRO G 60 104 7.12 CISPEP 34 VAL G 59 PRO G 60 105 -2.79 CISPEP 35 VAL G 59 PRO G 60 106 -10.17 CISPEP 36 VAL G 59 PRO G 60 107 -10.60 CISPEP 37 VAL G 59 PRO G 60 108 -2.01 CISPEP 38 VAL G 59 PRO G 60 109 -2.31 CISPEP 39 VAL G 59 PRO G 60 110 -8.32 CISPEP 40 VAL G 59 PRO G 60 111 -15.94 CISPEP 41 VAL G 59 PRO G 60 112 2.97 CISPEP 42 VAL G 59 PRO G 60 114 -14.42 CISPEP 43 VAL G 59 PRO G 60 115 -10.45 CISPEP 44 VAL G 59 PRO G 60 116 -25.05 CISPEP 45 VAL G 59 PRO G 60 117 -9.76 CISPEP 46 VAL G 59 PRO G 60 118 -22.65 CISPEP 47 VAL G 59 PRO G 60 119 -17.71 CISPEP 48 VAL G 59 PRO G 60 121 -1.00 CISPEP 49 VAL G 59 PRO G 60 122 -1.70 CISPEP 50 VAL G 59 PRO G 60 123 -12.34 CISPEP 51 VAL G 59 PRO G 60 124 4.39 CISPEP 52 VAL G 59 PRO G 60 125 12.01 CISPEP 53 VAL G 59 PRO G 60 126 -7.52 CISPEP 54 VAL G 59 PRO G 60 127 -25.80 CISPEP 55 VAL G 59 PRO G 60 128 18.00 CISPEP 56 VAL G 59 PRO G 60 129 -11.08 CISPEP 57 VAL G 59 PRO G 60 130 -9.20 CISPEP 58 VAL G 59 PRO G 60 131 -27.75 CISPEP 59 VAL G 59 PRO G 60 132 4.44 CISPEP 60 VAL G 59 PRO G 60 133 -17.48 CISPEP 61 VAL G 59 PRO G 60 134 -18.81 CISPEP 62 VAL G 59 PRO G 60 135 15.61 CISPEP 63 VAL G 59 PRO G 60 136 1.16 CISPEP 64 VAL G 59 PRO G 60 137 10.17 CISPEP 65 VAL G 59 PRO G 60 138 -11.31 CISPEP 66 VAL G 59 PRO G 60 139 7.04 CISPEP 67 VAL G 59 PRO G 60 140 -9.87

SITE 1 CC 4 CYS G 11 PRO G 12 TYR G 13 CYS G 14

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