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

(-) Description

Title :  CRYSTAL STRUCTURE OF D-SERINE DEHYDRATASE FROM CHICKEN KIDNEY
 
Authors :  H. Tanaka, M. Senda, N. Venugopalan, A. Yamamoto, T. Senda, T. Ishida, K
Date :  09 Sep 10  (Deposition) - 15 Jun 11  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Plp-Dependent Fold-Type Iii Enzyme, D-Serine Dehydratase, Plp Binding, Zinc Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Tanaka, M. Senda, N. Venugopalan, A. Yamamoto, T. Senda, T. Ishida, K. Horiike
Crystal Structure Of A Zinc-Dependent D-Serine Dehydratase From Chicken Kidney
J. Biol. Chem. V. 286 27548 2011
PubMed-ID: 21676877  |  Reference-DOI: 10.1074/JBC.M110.201160

(-) Compounds

Molecule 1 - D-SERINE DEHYDRATASE
    Chains: A
    EC Number: 4.3.1.18
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:43 , LYS A:45 , ALA A:86 , TYR A:174 , HIS A:176 , TYR A:181 , SER A:221 , THR A:222 , HIS A:239 , PRO A:240 , GLY A:241 , ASN A:242 , HOH A:594 , HOH A:617BINDING SITE FOR RESIDUE PLP A 401
2AC2SOFTWARELEU A:290 , HOH A:502BINDING SITE FOR RESIDUE CL A 450
3AC3SOFTWAREHIS A:347 , CYS A:349 , HOH A:616 , HOH A:617 , HOH A:634BINDING SITE FOR RESIDUE ZN A 451

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:183 -A:183

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:12 -Pro A:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ANU)

(-) 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:367
 aligned with A9CP13_CHICK | A9CP13 from UniProtKB/TrEMBL  Length:376

    Alignment length:376
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370      
         A9CP13_CHICK     1 MWLGALLDTLPTPALTIDRTTARRNAERMRERCRALGVRLRPHVKTHKTLEGGLLATGGTRRGIAVSTLAEARFFADGGFDDILLAYPVPTARLEECAGLARRLDAFHVLLDRPEALASLRQRPLGHGKRWLVWLKLDCGNGRAGVRPTDPAALELAQAIANDAPEEVTLVGVYAHCGNTYGCSGADTIQAIARTTTNAVLSFVAALRQAGVPCPQASIGSTPSCSHPIPEMSQLTELHPGNYIFYDLQQTQLGSCQPQDVAIRVLTRVIGHYAHRGQLLVDCGWAALSLHGAGAGQGPQGCAAIDGHPELRLVGLTQEHGLLEHAGGQMDFGRFPVGSVLALIPYHACATAAMHPVYYVHEEGKVVALWHPVRGW 376
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh...eeeeehhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhh....eeeee.hhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh........eeeeeee..--........hhhhhhhhhhhhhh....eeeeeeee.hhhhh-..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhh.hhhhhhh.ee..hhhhh.hhhhhhh...hhhhh.eeeeeeeeeee....eeee..hhhhhh.....---hhhh.eee......eeeee....eeee.---...........eeeeee.hhhhhhh....eeeee..eeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3anu A   1 MWLGALLDTLPTPALTIDRTTARRNAERMRERCRALGVRLRPHVKTHKTLEGGLLATGGTRRGIAVSTLAEARFFADGGFDDILLAYPVPTARLEECAGLARRLDAFHVLLDRPEALASLRQRPLGHGKRWLVWLKLDC--GRAGVRPTDPAALELAQAIANDAPEEVTLVGVYAHCGNTY-CSGADTIQAIARTTTNAVLSFVAALRQAGVPCPQASIGSTPSCSHPIPEMSQLTELHPGNYIFYDLQQTQLGSCQPQDVAIRVLTRVIGHYAHRGQLLVDCGWAALSLHGAG---GPQGCAAIDGHPELRLVGLTQEHGLLEH---QMDFGRFPVGSVLALIPYHACATAAMHPVYYVHEEGKVVALWHPVRGW 376
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |- |     150       160       170       180| |    190       200       210       220       230       240       250       260       270       280       290   |   300       310       320    |  330       340       350       360       370      
                                                                                                                                                                    139  |                                    181 |                                                                                                            294 298                        325 329                                               
                                                                                                                                                                       142                                      183
   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 3ANU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3ANU)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:12 - Pro A:13   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3anu
    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
  A9CP13_CHICK | A9CP13
    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)
  4.3.1.18
    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
  A9CP13_CHICK | A9CP13
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A9CP13_CHICK | A9CP13: 3anv 3awn 3awo

(-) Related Entries Specified in the PDB File

3anv