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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENOYL-COA HYDRATASE/ISOMERASE FROM XANTHOBACTER AUTOTROPHICUS PY2
 
Authors :  S. Eswaramoorthy, S. Chamala, B. Evans, F. Foti, A. Gizzi, B. Hillerich J. Lafleur, R. Seidel, G. Villigas, W. Zencheck, N. Al Obaidi, S. C. Al S. Swaminathan, New York Structural Genomics Research Consort (Nysgrc)
Date :  08 Apr 13  (Deposition) - 24 Apr 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Psi-Biology, Nysgrc, Structural Genomics, New York Structural Genomics Research Consortium, Dimer Of Trimers, Crotonase Superfamily, Oxyanion Hole, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. C. Almo, S. Swaminathan
Crystal Structure Of An Enoyl-Coa Hydratase/Isomerase From Xanthobacter Autotrophicus Py2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ENOYL-COA HYDRATASE/ISOMERASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: XAUT_3350
    Organism Scientific: XANTHOBACTER AUTOTROPHICUS
    Organism Taxid: 78245
    Strain: PY2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC
Biological Unit 2 (1x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 29)

Asymmetric Unit (3, 29)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE24Mod. Amino AcidSELENOMETHIONINE
3TLA3Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (3, 58)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE48Mod. Amino AcidSELENOMETHIONINE
3TLA6Ligand/IonL(+)-TARTARIC ACID
Biological Unit 2 (3, 29)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE24Mod. Amino AcidSELENOMETHIONINE
3TLA3Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:68 , GLY A:256 , LEU A:257 , ARG A:258 , HOH A:507 , HOH A:523BINDING SITE FOR RESIDUE TLA A 301
2AC2SOFTWAREARG A:181 , ARG A:194 , HIS A:198 , GLU C:165 , PRO C:269BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWAREGLY C:77 , VAL C:78 , GLY C:239 , ALA C:240 , HOH C:720 , HOH C:727 , HOH C:873BINDING SITE FOR RESIDUE TLA C 601
4AC4SOFTWAREGLY A:58 , ASN A:59 , HIS C:12 , ARG C:197 , HOH C:802 , HOH C:825 , HOH C:871BINDING SITE FOR RESIDUE TLA C 602
5AC5SOFTWAREGLN C:30 , PHE C:65 , GLN C:70 , TRP C:81 , ASP C:88 , HOH C:714 , HOH C:822BINDING SITE FOR RESIDUE GOL C 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K29)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K29)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K29)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K29)

(-) Exons   (0, 0)

(no "Exon" information available for 4K29)

(-) 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:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains d4k29a_ A: automated matches                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh......hhhhhhhhhhhhhhhhhh...eehhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k29 A   2 TYSKILYETLHGVARITLNRPERTNALDQEmLGEINAAmDAAEADAGVKAVIVRGAGNAFSSGFDLKAQmEARPAGVDAWRPLLRKDFDTVmRFWHCPKPTIAAVRGPCLAGACELALACDmTIATEDAFFGEPELKFGAGIVVmLLPWIVGPKIAKEIILLGEDRVPARRAAEIGmVNRVVDGDGLDAEALRIARHIGAIDPGLVKETKRALNRALETQGmLQALESALEIDLAIEGAGSPDKIAFFEVARRDGLRAAIAWRDARFPA 270
                                    11        21        31|       41        51        61        71        81        91 |     101       111       121 |     131       141    |  151       161       171      |181       191       201       211       221 |     231       241       251       261         
                                                         32-MSE  40-MSE                         71-MSE                93-MSE                       123-MSE                146-MSE                         178-MSE                                      223-MSE                                           


Chain B from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains d4k29b_ B: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh......hhhhhhhhhhhhhhhhhh...eehhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k29 B   3 YSKILYETLHGVARITLNRPERTNALDQEmLGEINAAmDAAEADAGVKAVIVRGAGNAFSSGFDLKAQmEARPAGVDAWRPLLRKDFDTVmRFWHCPKPTIAAVRGPCLAGACELALACDmTIATEDAFFGEPELKFGAGIVVmLLPWIVGPKIAKEIILLGEDRVPARRAAEIGmVNRVVDGDGLDAEALRIARHIGAIDPGLVKETKRALNRALETQGmLQALESALEIDLAIEGAGSPDKIAFFEVARRDGLRAAIAWRDARFPA 270
                                    12        22        32       |42        52        62        72        82        92|      102       112       122|      132       142   |   152       162       172     | 182       192       202       212       222|      232       242       252       262        
                                                        32-MSE  40-MSE                         71-MSE                93-MSE                       123-MSE                146-MSE                         178-MSE                                      223-MSE                                           


Chain C from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains d4k29c_ C: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh......hhhhhhhhhhhhhhhhhh...eehhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k29 C   3 YSKILYETLHGVARITLNRPERTNALDQEmLGEINAAmDAAEADAGVKAVIVRGAGNAFSSGFDLKAQmEARPAGVDAWRPLLRKDFDTVmRFWHCPKPTIAAVRGPCLAGACELALACDmTIATEDAFFGEPELKFGAGIVVmLLPWIVGPKIAKEIILLGEDRVPARRAAEIGmVNRVVDGDGLDAEALRIARHIGAIDPGLVKETKRALNRALETQGmLQALESALEIDLAIEGAGSPDKIAFFEVARRDGLRAAIAWRDARFPA 270
                                    12        22        32       |42        52        62        72        82        92|      102       112       122|      132       142   |   152       162       172     | 182       192       202       212       222|      232       242       252       262        
                                                        32-MSE  40-MSE                         71-MSE                93-MSE                       123-MSE                146-MSE                         178-MSE                                      223-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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K29)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K29)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4k29)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  4k29
    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
  A7IKN6_XANP2 | A7IKN6
    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
  A7IKN6_XANP2 | A7IKN6
    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 4K29)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4K29)