1UQM - Header Asymmetric Unit

HEADER OXIDOREDUCTASE 15-OCT-03 1UQM

TITLE REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY MODELS 46-90

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 1UQ9, 1UQP, 1UQO AND 1UQQ

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 1UQM 1 JRNL REVDAT 1 06-NOV-03 1UQM 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 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 1UQM COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI ON 20-OCT-2003. REMARK 100 THE EBI ID CODE IS EBI-13734.

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: 1UQ9 : MODELS REMARK 400 1 - 45 1UQP : MODELS 91 - 135 1UQO : MODELS 136 - 180 1UQQ REMARK 400 : MODELS 181 - 225 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 46 ALA G 59 -34.32 77.82 REMARK 500 50 ALA G 59 -56.45 72.72 REMARK 500 52 ALA G 59 -38.87 68.31 REMARK 500 53 ALA G 59 -34.10 81.82 REMARK 500 60 ALA G 59 -31.97 85.37 REMARK 500 66 ALA G 37 -115.70 -150.73 REMARK 500 66 ALA G 38 -106.06 50.24 REMARK 500 69 ALA G 38 -89.84 31.29 REMARK 500 80 ALA G 59 -34.74 80.10 REMARK 500 82 ALA G 59 -40.37 91.62 REMARK 500 83 ALA G 59 -57.38 85.19 REMARK 500 84 ALA G 59 -45.31 86.28 REMARK 500 85 ALA G 59 -61.12 72.61 REMARK 500 86 ALA G 59 -30.83 77.59 REMARK 500 87 ALA G 59 -56.97 90.01 REMARK 500 88 ALA G 38 -109.27 65.93 REMARK 500 89 ALA G 59 -54.01 95.72 REMARK 500 90 ALA G 59 -34.03 74.42 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 7 LYS G 8 46 148.02 REMARK 500 THR G 7 LYS G 8 48 147.73 REMARK 500 ARG G 40 GLU G 41 59 149.69 REMARK 500 THR G 7 LYS G 8 61 147.37 REMARK 500 THR G 7 LYS G 8 62 149.19 REMARK 500 THR G 7 LYS G 8 64 144.25 REMARK 500 ASN G 36 ALA G 37 64 -147.69 REMARK 500 THR G 7 LYS G 8 65 146.11 REMARK 500 SER G 47 GLY G 48 70 -148.93 REMARK 500 VAL G 52 PRO G 53 70 -34.43 REMARK 500 THR G 7 LYS G 8 88 148.82

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: 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 91-135 REMARK 900 RELATED ID: 1UQK RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY REMARK 900 MODELS 136-180 REMARK 900 RELATED ID: 1UQL RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY REMARK 900 MODELS 180-225 REMARK 900 RELATED ID: 1UQ9 RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY REMARK 900 MODELS 1-45 REMARK 900 RELATED ID: 1UQP RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY REMARK 900 MODELS 91-135 REMARK 900 RELATED ID: 1UQO RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY REMARK 900 MODELS 136-180 REMARK 900 RELATED ID: 1UQQ RELATED DB: PDB REMARK 900 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY REMARK 900 MODELS 180-225 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

DBREF 1UQM 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 ASN G 36 GLY G 48 1 13 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 46 2.68 CISPEP 2 VAL G 52 PRO G 53 47 -7.78 CISPEP 3 VAL G 52 PRO G 53 48 13.44 CISPEP 4 VAL G 52 PRO G 53 49 -13.09 CISPEP 5 VAL G 52 PRO G 53 50 4.86 CISPEP 6 VAL G 52 PRO G 53 51 -4.87 CISPEP 7 VAL G 52 PRO G 53 52 13.70 CISPEP 8 VAL G 52 PRO G 53 53 -9.26 CISPEP 9 VAL G 52 PRO G 53 54 2.44 CISPEP 10 VAL G 52 PRO G 53 55 6.61 CISPEP 11 VAL G 52 PRO G 53 56 1.17 CISPEP 12 VAL G 52 PRO G 53 57 -12.39 CISPEP 13 VAL G 52 PRO G 53 58 20.29 CISPEP 14 VAL G 52 PRO G 53 59 -0.35 CISPEP 15 VAL G 52 PRO G 53 60 15.17 CISPEP 16 VAL G 52 PRO G 53 61 -0.85 CISPEP 17 VAL G 52 PRO G 53 62 -9.27 CISPEP 18 VAL G 52 PRO G 53 63 -11.62 CISPEP 19 VAL G 52 PRO G 53 64 -16.74 CISPEP 20 VAL G 52 PRO G 53 65 -15.63 CISPEP 21 VAL G 52 PRO G 53 66 4.42 CISPEP 22 VAL G 52 PRO G 53 67 -11.06 CISPEP 23 VAL G 52 PRO G 53 68 2.29 CISPEP 24 VAL G 52 PRO G 53 69 -19.12 CISPEP 25 VAL G 52 PRO G 53 71 -12.50 CISPEP 26 VAL G 52 PRO G 53 72 -19.03 CISPEP 27 VAL G 52 PRO G 53 73 -24.80 CISPEP 28 VAL G 52 PRO G 53 74 -6.76 CISPEP 29 VAL G 52 PRO G 53 75 -7.07 CISPEP 30 VAL G 52 PRO G 53 76 -4.80 CISPEP 31 VAL G 52 PRO G 53 77 -16.24 CISPEP 32 VAL G 52 PRO G 53 78 -4.89 CISPEP 33 VAL G 52 PRO G 53 79 -24.53 CISPEP 34 VAL G 52 PRO G 53 80 -8.19 CISPEP 35 VAL G 52 PRO G 53 81 -6.70 CISPEP 36 VAL G 52 PRO G 53 82 -23.11 CISPEP 37 VAL G 52 PRO G 53 83 -17.64 CISPEP 38 VAL G 52 PRO G 53 84 -23.70 CISPEP 39 VAL G 52 PRO G 53 85 -5.56 CISPEP 40 VAL G 52 PRO G 53 86 -22.18 CISPEP 41 VAL G 52 PRO G 53 87 -28.18 CISPEP 42 VAL G 52 PRO G 53 88 -6.25 CISPEP 43 VAL G 52 PRO G 53 89 -14.91 CISPEP 44 VAL G 52 PRO G 53 90 -18.99

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