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(-) Description

Title :  REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY MODELS 136-180
 
Authors :  N. Foloppe, L. Nilsson
Date :  15 Oct 03  (Deposition) - 06 Nov 03  (Release) - 19 Feb 04  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  G  (45x)
Keywords :  Electron Transport, Oxidoreductase, Deoxyribonucleotide Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Foloppe, L. Nilsson
The Glutaredoxin-C-P-Y-C- Motif; Influence Of Peripheral Residues
Structure V. 12 289 2004
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAREDOXIN 3
    Chains: G
    Organism Scientific: ESCHERICHIA COLI
    Other Details: MODEL, 225 STRUCTURES FROM 50 NS MD SIMULATION. THIS ENTRY HAS 45 MODELS. THE OTHER ENTRIES ARE 1UQ8, 1UQI, 1UQK AND 1UQL
    Other Details - Source: INITIAL MODEL COORDINATES TAKEN FROM 3GRX SEE ALSO MODEL STRUCTURE 1ILB
    Synonym: GRX3

 Structural Features

(-) Chains, Units

  
Theoretical Model (45x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1UQJ)

(-) Sites  (1, 1)

Theoretical Model (1, 1)
No.NameEvidenceResiduesDescription
1CCnot definedCYS G:11 , PRO G:12 , TYR G:13 , CYS G:14CYS 11 (THIOLATE) AND CYS 14 ARE THE ACTIVE CYSTEINS INVOLVED IN DISULFIDE FORMATION

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UQJ)

(-) Cis Peptide Bonds  (1, 44)

Theoretical Model
No.ModelResidues
1136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180Val G:52 -Pro G:53

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UQJ)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_1PS00195 Glutaredoxin active site.GLRX3_ECO576-22  1G:5-21
GLRX3_ECOL66-22  1G:5-21
GLRX3_ECOLI6-22  1G:5-21

(-) Exons   (0, 0)

(no "Exon" information available for 1UQJ)

(-) Sequences/Alignments

Theoretical Model
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain G from PDB  Type:PROTEIN  Length:82
 aligned with GLRX3_ECO57 | P0AC64 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:82
                                    11        21        31        41        51        61        71        81  
           GLRX3_ECO57    2 ANVEIYTKETCPYCHRAKALLSSKGVSFQELPIDGNAAKREEMIKRSGRTTVPQIFIDAQHIGGCDDLYALDARGGLDPLLK 83
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhh.........eeee..eeeehhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----GLUTAREDOXIN_1   ------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  1uqj G  1 ANVEIYTKETCPYCHRAKALLSSKGVSFQELPIDGNAAKREEMIKRSGRTTVPQIFIDAQHIGGCDDLYALDARGGLDPLLK 82
                                    10        20        30        40        50        60        70        80  


Chain G from PDB  Type:PROTEIN  Length:82
 aligned with GLRX3_ECOL6 | P0AC63 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:82
                                    11        21        31        41        51        61        71        81  
           GLRX3_ECOL6    2 ANVEIYTKETCPYCHRAKALLSSKGVSFQELPIDGNAAKREEMIKRSGRTTVPQIFIDAQHIGGCDDLYALDARGGLDPLLK 83
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhh.........eeee..eeeehhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----GLUTAREDOXIN_1   ------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  1uqj G  1 ANVEIYTKETCPYCHRAKALLSSKGVSFQELPIDGNAAKREEMIKRSGRTTVPQIFIDAQHIGGCDDLYALDARGGLDPLLK 82
                                    10        20        30        40        50        60        70        80  


Chain G from PDB  Type:PROTEIN  Length:82
 aligned with GLRX3_ECOLI | P0AC62 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:82
                                    11        21        31        41        51        61        71        81  
           GLRX3_ECOLI    2 ANVEIYTKETCPYCHRAKALLSSKGVSFQELPIDGNAAKREEMIKRSGRTTVPQIFIDAQHIGGCDDLYALDARGGLDPLLK 83
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhh.........eeee..eeeehhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----GLUTAREDOXIN_1   ------------------------------------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  1uqj G  1 ANVEIYTKETCPYCHRAKALLSSKGVSFQELPIDGNAAKREEMIKRSGRTTVPQIFIDAQHIGGCDDLYALDARGGLDPLLK 82
                                    10        20        30        40        50        60        70        80
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1UQJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1UQJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1UQJ)

(-) Gene Ontology  (8, 19)

Theoretical Model(hide GO term definitions)
Chain G   (GLRX3_ECOLI | P0AC62)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0043295    glutathione binding    Interacting selectively and non-covalently with glutathione; a tripeptide composed of the three amino acids cysteine, glutamic acid and glycine.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0009263    deoxyribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain G   (GLRX3_ECOL6 | P0AC63)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0009263    deoxyribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Chain G   (GLRX3_ECO57 | P0AC64)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0009263    deoxyribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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    Val G:52 - Pro G:53   [ RasMol ]  
 

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  GLRX3_ECOL6 | P0AC63
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GLRX3_ECO57 | P0AC64: 1uq8 1uq9 1uqi 1uqk 1uql 1uqm 1uqo 1uqp 1uqq
        GLRX3_ECOL6 | P0AC63: 1uq8 1uq9 1uqi 1uqk 1uql 1uqm 1uqo 1uqp 1uqq
        GLRX3_ECOLI | P0AC62: 1fov 1ilb 1uq8 1uq9 1uqi 1uqk 1uql 1uqm 1uqo 1uqp 1uqq 3grx

(-) Related Entries Specified in the PDB File

1fov GLUTAREDOXIN 3 FROM ESCHERICHIA COLI IN THE FULLY OXIDIZEDFORM
1ilb THEORETICAL MODEL OF REDUCED E. COLI GLUTAREDOXIN 3
1uq8 REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY, MODELS 1-45
1uqi REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY, MODELS 46-90
1uqk REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY, MODELS 91-135
1uql REDUCED GLUTAREDOXIN 3 SIMULATION TRAJECTORY, MODELS 180-225
3grx NMR STRUCTURE OF ESCHERICHIA COLI GLUTAREDOXIN 3-GLUTATHIONE MIXED DISULFIDE COMPLEX, 20 STRUCTURES