Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ISOCHORISMATASE FAMILY PROTEIN FROM DESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. HILDENBOROUGH
 
Authors :  V. N. Malashkevich, R. Toro, C. Morano, J. M. Sauder, S. K. Burley, S. C. A York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  12 Jun 09  (Deposition) - 30 Jun 09  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (2x),B (2x)
Keywords :  Structural Genomics, Crystal Structure, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Isochorismatase Hydrolase. Desulfovibrio Vulgaris, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, C. Morano, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Isochorismatase Family Protein From Desulfovibrio Vulgaris Subsp. Vulgaris Str. Hildenborough
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ISOCHORISMATASE FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DVU_0033
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): A (2x)B (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3HU5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HU5)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:76 -Glu A:77
2Glu A:77 -Gly A:78
3Thr A:134 -Gln A:135
4Thr B:134 -Gln B:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HU5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HU5)

(-) Exons   (0, 0)

(no "Exon" information available for 3HU5)

(-) Sequences/Alignments

Asymmetric 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:190
 aligned with Q72G28_DESVH | Q72G28 from UniProtKB/TrEMBL  Length:204

    Alignment length:190
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193
         Q72G28_DESVH     4 NRTVALAIIDMQNDFVLPGAPACVEGAMGTVPVIAGLLAKARAEGWMVLHVVRAHRADGSDAEKSREHLFLEGGGLCVAGTPGAEIVAGLEPASGETVLVKTRFSAFMGTECDMLLRRRGVDTLLVSGTQYPNCIRGTAVDAFALDYDVVVVTDACSARTPGVAESNINDMRAMGITCVPLTALDDVLAR 193
               SCOP domains d3hu5a_ A: automated matches                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhh........hhhhhhhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhh.........hhhhh...........eeee..........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhhh.eeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hu5 A   6 NRTVALAIIDmQNDFVLPGAPACVEGAmGTVPVIAGLLAKARAEGWmVLHVVRAHRADGSDAEKSREHLFLEGGGLCVAGTPGAEIVAGLEPASGETVLVKTRFSAFmGTECDmLLRRRGVDTLLVSGTQYPNCIRGTAVDAFALDYDVVVVTDACSARTPGVAESNINDmRAmGITCVPLTALDDVLAR 195
                                    15|       25       |35        45      | 55        65        75        85        95       105       115   |   125       135       145       155       165       175|  |   185       195
                                     16-MSE           33-MSE             52-MSE                                                      113-MSE |                                                      176-MSE               
                                                                                                                                           119-MSE                                                     179-MSE            


Chain B from PDB  Type:PROTEIN  Length:190
 aligned with Q72G28_DESVH | Q72G28 from UniProtKB/TrEMBL  Length:204

    Alignment length:190
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193
         Q72G28_DESVH     4 NRTVALAIIDMQNDFVLPGAPACVEGAMGTVPVIAGLLAKARAEGWMVLHVVRAHRADGSDAEKSREHLFLEGGGLCVAGTPGAEIVAGLEPASGETVLVKTRFSAFMGTECDMLLRRRGVDTLLVSGTQYPNCIRGTAVDAFALDYDVVVVTDACSARTPGVAESNINDMRAMGITCVPLTALDDVLAR 193
               SCOP domains d3hu5b_ B: automated matches                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhh.........hhhhhhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhh.........................eeee..........hhhhhhhhhh..eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhhh.eeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hu5 B   6 NRTVALAIIDmQNDFVLPGAPACVEGAmGTVPVIAGLLAKARAEGWmVLHVVRAHRADGSDAEKSREHLFLEGGGLCVAGTPGAEIVAGLEPASGETVLVKTRFSAFmGTECDmLLRRRGVDTLLVSGTQYPNCIRGTAVDAFALDYDVVVVTDACSARTPGVAESNINDmRAmGITCVPLTALDDVLAR 195
                                    15|       25       |35        45      | 55        65        75        85        95       105       115   |   125       135       145       155       165       175|  |   185       195
                                     16-MSE           33-MSE             52-MSE                                                      113-MSE |                                                      176-MSE               
                                                                                                                                           119-MSE                                                     179-MSE
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HU5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HU5)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q72G28_DESVH | Q72G28)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3hu5)
 
  Cis Peptide Bonds
    Glu A:77 - Gly A:78   [ RasMol ]  
    Leu A:76 - Glu A:77   [ RasMol ]  
    Thr A:134 - Gln A:135   [ RasMol ]  
    Thr B:134 - Gln B:135   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3hu5
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q72G28_DESVH | Q72G28
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q72G28_DESVH | Q72G28
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3HU5)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3HU5)