1UQK - Header Asymmetric Unit

HEADER OXIDOREDUCTASE 15-OCT-03 1UQK

TITLE REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY MODELS 91-135

COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN 3; COMPND 3 CHAIN: G; COMPND 4 SYNONYM: GRX3; COMPND 5 OTHER_DETAILS: MODEL, 225 STRUCTURES FROM 50 NS MD COMPND 6 SIMULATION. THIS ENTRY HAS 45 MODELS. THE OTHER ENTRIES COMPND 7 ARE 1UQ8, 1UQI, 1UQJ AND 1UQL

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 OTHER_DETAILS: INITIAL MODEL COORDINATES TAKEN FROM 3GRX; SOURCE 4 SEE ALSO MODEL STRUCTURE 1ILB

KEYWDS ELECTRON TRANSPORT, OXIDOREDUCTASE, DEOXYRIBONUCLEOTIDE KEYWDS 2 SYNTHESIS

EXPDTA THEORETICAL MODEL

AUTHOR N.FOLOPPE,L.NILSSON

REVDAT 2 19-FEB-04 1UQK 1 JRNL REVDAT 1 06-NOV-03 1UQK 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 US ISSN 0969-2126

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.FOLOPPE,J.SAGEMARK,K.NORDSTRAND,K.D.BERNDT REMARK 1 TITL STRUCTURE, DYNAMICS AND ELECTROSTATICS OF THE REMARK 1 TITL 2 ACTIVE SITE OF GLUTAREDOXIN 3 FROM ESCHERICHIA REMARK 1 TITL 3 COLI: COMPARISON WITH FUNCTIONALLY RELATED PROTEINS REMARK 1 REF J.MOL.BIOL. V. 310 449 2001 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836

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

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI ON 17-OCT-2003. REMARK 100 THE EBI ID CODE IS EBI-13731.

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 1 OF 5 (225 MODELS ALTOGETHER). REMARK 400 THIS ENTRY CONTAINS 45 MODELS OF THE TIME COURSE MD REMARK 400 SIMULATION. THE OTHER ENTRIES ARE AS FOLLOWS: 1UQ8 : MODELS REMARK 400 1 - 45 1UQI : MODELS 46 - 90 1UQJ : MODELS 136 - 180 1UQL : REMARK 400 MODELS 181 - 225 FUNCTION: THE DISULFIDE BOND FUNCTIONS AS REMARK 400 AN ELECTRON CARRIER IN THE GLUTATHIONE-DEPENDENT SYNTHESIS REMARK 400 OF DEOXYRIBONUCLEOTIDES BY T ENZYME RIBONUCLEOTIDE REMARK 400 REDUCTASE. IN ADDITION, IT IS ALSO INVOLVE IN REDUCING SOME REMARK 400 DISULFIDES IN A COUPLED SYSTEM WITH 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 91 ASP G 58 -104.38 38.11 REMARK 500 92 ASP G 58 -108.35 62.19 REMARK 500 93 ASP G 58 -98.54 51.26 REMARK 500 95 ASP G 58 -104.06 53.45 REMARK 500 96 ASP G 58 -115.33 62.07 REMARK 500 97 ASP G 58 -105.12 63.57 REMARK 500 98 ASP G 58 -83.02 54.24 REMARK 500 99 ASP G 58 -105.20 58.29 REMARK 500 100 ASP G 58 -98.38 67.15 REMARK 500 101 ASP G 58 -115.50 53.01 REMARK 500 102 ASP G 58 -114.91 53.72 REMARK 500 103 ASP G 58 -101.71 78.77 REMARK 500 104 ASP G 58 -110.44 45.15 REMARK 500 105 ASP G 58 -116.55 71.30 REMARK 500 106 ASP G 58 -78.74 60.28 REMARK 500 107 ASP G 58 -108.26 66.08 REMARK 500 108 ASP G 58 -97.54 63.12 REMARK 500 109 ASP G 58 -92.33 61.46 REMARK 500 110 ASP G 58 -100.27 65.33 REMARK 500 111 ASP G 58 -119.35 50.65 REMARK 500 113 ASP G 58 -115.08 56.49 REMARK 500 114 ASP G 58 -105.91 43.88 REMARK 500 115 ASP G 58 -105.13 66.51 REMARK 500 116 ASP G 58 -107.76 52.82 REMARK 500 117 ASP G 58 -115.01 53.14 REMARK 500 118 ASP G 58 -104.89 46.60 REMARK 500 119 ASP G 58 -103.81 57.59 REMARK 500 120 ASP G 58 -110.43 49.33 REMARK 500 121 ASP G 58 -117.51 41.94 REMARK 500 122 ASP G 58 -94.97 59.94 REMARK 500 123 ASP G 58 -111.18 60.58 REMARK 500 124 ASP G 58 -108.62 62.25 REMARK 500 125 ASP G 58 -98.74 73.19 REMARK 500 126 ASP G 58 -104.71 60.30 REMARK 500 127 ASP G 58 -115.68 57.75 REMARK 500 128 ASP G 58 -104.27 61.67 REMARK 500 129 ASP G 58 -95.66 50.53 REMARK 500 130 ASP G 58 -87.02 57.09 REMARK 500 131 ASP G 58 -116.00 61.13 REMARK 500 132 ASP G 58 -98.48 61.29 REMARK 500 133 ASP G 58 -116.38 56.65 REMARK 500 134 ASP G 58 -104.83 62.66 REMARK 500 135 ASP G 58 -91.16 43.84 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 THR G 51 VAL G 52 93 143.10 REMARK 500 PRO G 79 LEU G 80 103 148.64 REMARK 500 GLY G 48 ARG G 49 117 -148.64 REMARK 500 TYR G 6 THR G 7 125 -142.93 REMARK 500 MET G 43 ILE G 44 133 -148.07

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

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FOV RELATED DB: PDB REMARK 900 GLUTAREDOXIN 3 FROM ESCHERICHIA COLI IN THE REMARK 900 FULLY OXIDIZEDFORM REMARK 900 RELATED ID: 1ILB RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF REDUCED E. COLI REMARK 900 GLUTAREDOXIN 3 REMARK 900 RELATED ID: 3GRX RELATED DB: PDB REMARK 900 NMR STRUCTURE OF ESCHERICHIA COLI GLUTAREDOXIN REMARK 900 3-GLUTATHIONE MIXED DISULFIDE COMPLEX, 20 REMARK 900 STRUCTURES REMARK 900 RELATED ID: 1UQ8 RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY, REMARK 900 MODELS 1-45 REMARK 900 RELATED ID: 1UQI RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY, REMARK 900 MODELS 46-90 REMARK 900 RELATED ID: 1UQJ RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY, REMARK 900 MODELS 135-180 REMARK 900 RELATED ID: 1UQL RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY, REMARK 900 MODELS 180-225

DBREF 1UQK G 1 82 UNP P37687 GLR3_ECOLI 1 82

SEQRES 1 G 82 ALA ASN VAL GLU ILE TYR THR LYS GLU THR CYS PRO TYR SEQRES 2 G 82 CYS HIS ARG ALA LYS ALA LEU LEU SER SER LYS GLY VAL SEQRES 3 G 82 SER PHE GLN GLU LEU PRO ILE ASP GLY ASN ALA ALA LYS SEQRES 4 G 82 ARG GLU GLU MET ILE LYS ARG SER GLY ARG THR THR VAL SEQRES 5 G 82 PRO GLN ILE PHE ILE ASP ALA GLN HIS ILE GLY GLY CYS SEQRES 6 G 82 ASP ASP LEU TYR ALA LEU ASP ALA ARG GLY GLY LEU ASP SEQRES 7 G 82 PRO LEU LEU LYS

HELIX 1 1 CYS G 11 GLY G 25 1 15 HELIX 2 2 LYS G 39 LYS G 45 1 7 HELIX 3 3 GLY G 64 GLY G 75 1 12 HELIX 4 4 LEU G 77 LYS G 82 1 6

SHEET 1 GA 4 GLN G 29 PRO G 32 0 SHEET 2 GA 4 VAL G 3 THR G 7 1 O VAL G 3 N GLN G 29 SHEET 3 GA 4 GLN G 54 ILE G 57 -1 O GLN G 54 N TYR G 6 SHEET 4 GA 4 GLN G 60 GLY G 63 -1 O GLN G 60 N ILE G 57

CISPEP 1 VAL G 52 PRO G 53 91 14.50 CISPEP 2 VAL G 52 PRO G 53 92 -2.77 CISPEP 3 VAL G 52 PRO G 53 93 -4.37 CISPEP 4 VAL G 52 PRO G 53 94 -2.32 CISPEP 5 VAL G 52 PRO G 53 95 -23.20 CISPEP 6 VAL G 52 PRO G 53 96 -0.04 CISPEP 7 VAL G 52 PRO G 53 97 8.69 CISPEP 8 VAL G 52 PRO G 53 98 10.67 CISPEP 9 VAL G 52 PRO G 53 99 10.46 CISPEP 10 VAL G 52 PRO G 53 100 2.46 CISPEP 11 VAL G 52 PRO G 53 101 -0.62 CISPEP 12 VAL G 52 PRO G 53 102 9.83 CISPEP 13 VAL G 52 PRO G 53 103 -13.59 CISPEP 14 VAL G 52 PRO G 53 104 -18.81 CISPEP 15 VAL G 52 PRO G 53 105 2.35 CISPEP 16 VAL G 52 PRO G 53 106 -0.11 CISPEP 17 VAL G 52 PRO G 53 107 -1.77 CISPEP 18 VAL G 52 PRO G 53 108 -13.54 CISPEP 19 VAL G 52 PRO G 53 109 -8.74 CISPEP 20 VAL G 52 PRO G 53 110 3.38 CISPEP 21 VAL G 52 PRO G 53 111 4.67 CISPEP 22 VAL G 52 PRO G 53 112 -3.10 CISPEP 23 VAL G 52 PRO G 53 113 -15.68 CISPEP 24 VAL G 52 PRO G 53 114 -7.04 CISPEP 25 VAL G 52 PRO G 53 115 10.52 CISPEP 26 VAL G 52 PRO G 53 116 -2.28 CISPEP 27 VAL G 52 PRO G 53 117 -5.09 CISPEP 28 VAL G 52 PRO G 53 118 5.40 CISPEP 29 VAL G 52 PRO G 53 119 16.81 CISPEP 30 VAL G 52 PRO G 53 120 5.86 CISPEP 31 VAL G 52 PRO G 53 121 10.87 CISPEP 32 VAL G 52 PRO G 53 122 24.25 CISPEP 33 VAL G 52 PRO G 53 123 23.03 CISPEP 34 VAL G 52 PRO G 53 124 17.24 CISPEP 35 VAL G 52 PRO G 53 125 2.36 CISPEP 36 VAL G 52 PRO G 53 126 5.25 CISPEP 37 VAL G 52 PRO G 53 127 3.45 CISPEP 38 VAL G 52 PRO G 53 128 4.34 CISPEP 39 VAL G 52 PRO G 53 129 14.87 CISPEP 40 VAL G 52 PRO G 53 130 20.92 CISPEP 41 VAL G 52 PRO G 53 131 14.28 CISPEP 42 VAL G 52 PRO G 53 132 -3.99 CISPEP 43 VAL G 52 PRO G 53 133 -2.18 CISPEP 44 VAL G 52 PRO G 53 134 14.95 CISPEP 45 VAL G 52 PRO G 53 135 22.63

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