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

(-) Description

Title :  STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE WILD TYPE HUMAN ENZYME.
 
Authors :  C. G. Amrich, A. A. Aslam, A. Heroux, A. P. Vandemark
Date :  25 Feb 14  (Deposition) - 14 Jan 15  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Alpha/Beta Barrel, Tim Barrel, Isomerase, Glycolytic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. P. Roland, C. G. Amrich, C. J. Kammerer, K. A. Stuchul, S. B. Larsen, S. Rode, A. A. Aslam, A. Heroux, R. Wetzel, A. P. Vandemark, M. J. Palladino
Triosephosphate Isomerase I170V Alters Catalytic Site, Enhances Stability And Induces Pathology In A Drosophila Model Of Tpi Deficiency.
Biochim. Biophys. Acta V. 1852 61 2015
PubMed-ID: 25463631  |  Reference-DOI: 10.1016/J.BBADIS.2014.10.010

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLC3
    Expression System Strain: BL21(DE3) CODON+RILP
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TPI, TPI1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TIM, TRIOSE-PHOSPHATE ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1BR2Ligand/IonBROMIDE ION
2K2Ligand/IonPOTASSIUM ION
3NA1Ligand/IonSODIUM ION
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:221 , GLN A:223 , VAL A:226 , HOH A:519BINDING SITE FOR RESIDUE K A 301
2AC2SOFTWAREALA A:169 , GLY A:171 , THR A:172 , GLY A:173 , LYS A:174 , HOH B:444BINDING SITE FOR RESIDUE NA A 302
3AC3SOFTWAREASN A:71 , THR A:175 , HOH A:557BINDING SITE FOR RESIDUE BR A 303
4AC4SOFTWARELYS B:13 , ALA B:169 , ILE B:170 , GLY B:171 , GLY B:210 , SER B:211 , GLY B:232 , GLY B:233 , BR B:303 , HOH B:409 , HOH B:411 , HOH B:477 , HOH B:481BINDING SITE FOR RESIDUE PO4 B 301
5AC5SOFTWAREALA B:221 , GLN B:223 , VAL B:226 , HOH B:440 , HOH B:462 , HOH B:493 , HOH B:503BINDING SITE FOR RESIDUE K B 302
6AC6SOFTWAREASN B:11 , HIS B:95 , GLU B:165 , PO4 B:301BINDING SITE FOR RESIDUE BR B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4POC)

(-) 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:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh...hhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhh.....eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4poc A   3 SRKFFVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      


Chain B from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhh.....eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4poc B   2 PSRKFFVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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 4POC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    BR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4poc)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4poc
    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
  TPIS_HUMAN | P60174
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.3.1.1
    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
  TPIS_HUMAN | P60174
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TPIS_HUMAN | P60174: 1hti 1klg 1klu 1wyi 2iam 2ian 2jk2 2vom 4br1 4e41 4pod 4unk 4unl 4zvj

(-) Related Entries Specified in the PDB File

4pod STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE I170V MUTANT HUMAN ENZYME.