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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX
 
Authors :  M. A. Walsh, A. Mccarthy, P. A. O'Farrell, P. Mccardle, P. D. Cunningham S. G. Mayhew, T. M. Higgins
Date :  12 Sep 98  (Deposition) - 09 Feb 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Flavoprotein, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Walsh, A. Mccarthy, P. A. O'Farrell, P. Mcardle, P. D. Cunningham S. G. Mayhew, T. M. Higgins
X-Ray Crystal Structure Of The Desulfovibrio Vulgaris (Hildenborough) Apoflavodoxin-Riboflavin Complex.
Eur. J. Biochem. V. 258 362 1998
PubMed-ID: 9874201  |  Reference-DOI: 10.1046/J.1432-1327.1998.2580362.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (FLAVODOXIN)
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainTG1
    Expression System Taxid562
    Organism ScientificDESULFOVIBRIO VULGARIS
    Organism Taxid881

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1RBF2Ligand/IonRIBOFLAVIN
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:10 , THR A:11 , THR A:12 , GLY A:13 , ASN A:14 , THR A:15 , SER A:58 , RBF A:301BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWARESER B:10 , THR B:11 , THR B:12 , GLY B:13 , ASN B:14 , THR B:15 , SER B:58 , HOH B:338BINDING SITE FOR RESIDUE SO4 B 202
3AC3SOFTWAREASN A:14 , THR A:59 , TRP A:60 , GLY A:61 , CYS A:93 , GLY A:94 , ASP A:95 , TYR A:98 , TYR A:100 , PHE A:101 , CYS A:102 , SO4 A:201 , HOH A:321 , HOH A:331 , HOH A:333 , HOH A:343 , HOH A:374BINDING SITE FOR RESIDUE RBF A 301
4AC4SOFTWAREASN B:14 , THR B:59 , TRP B:60 , GLY B:61 , GLY B:94 , ASP B:95 , TYR B:98 , TYR B:100 , PHE B:101 , CYS B:102 , HOH B:312 , HOH B:317 , HOH B:334 , HOH B:338BINDING SITE FOR RESIDUE RBF B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BU5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BU5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BU5)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FLAVODOXIN_LIKEPS50902 Flavodoxin-like domain profile.FLAV_DESVH4-145
 
  2A:4-145
B:4-145
2FLAVODOXINPS00201 Flavodoxin signature.FLAV_DESVH6-22
 
  2A:6-22
B:6-22

(-) Exons   (0, 0)

(no "Exon" information available for 1BU5)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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 A from PDB  Type:PROTEIN  Length:147
 aligned with FLAV_DESVH | P00323 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           FLAV_DESVH     2 PKALIVYGSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQDDFIPLFDSLEETGAQGRKVACFGCGDSSYEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAI 148
               SCOP domains d1bu5a_ A: Flavodoxin                                                                                                                               SCOP domains
               CATH domains 1bu5A00 A:2-148  [code=3.40.50.360, no name defined]                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhh..eeeeeehhh...........eeeeee..............hhhhhhhhh.......eeeeeee........hhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --FLAVODOXIN_LIKE  PDB: A:4-145 UniProt: 4-145                                                                                                  --- PROSITE (1)
                PROSITE (2) ----FLAVODOXIN       ------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bu5 A   2 PKALIVYGSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQDDFIPLFDSLEETGAQGRKVACFGCGDSSYEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAI 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with FLAV_DESVH | P00323 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           FLAV_DESVH     2 PKALIVYGSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQDDFIPLFDSLEETGAQGRKVACFGCGDSSYEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAI 148
               SCOP domains d1bu5b_ B: Flavodoxin                                                                                                                               SCOP domains
               CATH domains 1bu5B00 B:2-148  [code=3.40.50.360, no name defined]                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhh...eeeeeehhh...........eeeeee...........hhhhhhhhhhhh.......eeeeeee........hhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --FLAVODOXIN_LIKE  PDB: B:4-145 UniProt: 4-145                                                                                                  --- PROSITE (1)
                PROSITE (2) ----FLAVODOXIN       ------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bu5 B   2 PKALIVYGSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQDDFIPLFDSLEETGAQGRKVACFGCGDSSYEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAI 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BU5)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FLAV_DESVH | P00323)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    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.
biological process
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FLAV_DESVH | P003231akq 1akr 1akt 1aku 1akv 1akw 1azl 1c7e 1c7f 1f4p 1fx1 1i1o 1j8q 1j9e 1j9g 1wsb 1wsw 1xt6 1xyv 1xyy 2fx2 3fx2 4fx2 5fx2 5tgz 5v56 5v57 5xr8 5xra

(-) Related Entries Specified in the PDB File

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