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 4-PHENYLIMIDAZOLE BOUND FORM OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE (G262A MUTANT)
 
Authors :  H. Sugimoto, M. Horitani, E. Kometani, Y. Shiro
Date :  30 Jul 14  (Deposition) - 02 Sep 15  (Release) - 02 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metal-Binding, All Alpha, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Horitani, E. Kometani, E. Vottero, T. Otsuki, Y. Shiro, H. Sugimoto
Conformation And Mobility Of Active Site Loop Is Critical For Substrate Binding And Inhibition In Human Indoleamine 2, 3-Dioxygenase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INDOLEAMINE 2,3-DIOXYGENASE 1
    Chains: A, B
    EC Number: 1.13.11.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3) CODONPLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IDO1, IDO, INDO
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IDO-1,INDOLEAMINE-PYRROLE 2,3-DIOXYGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NHE4Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3PIM2Ligand/Ion4-PHENYL-1H-IMIDAZOLE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NHE2Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3PIM1Ligand/Ion4-PHENYL-1H-IMIDAZOLE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NHE2Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3PIM1Ligand/Ion4-PHENYL-1H-IMIDAZOLE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:126 , PHE A:163 , SER A:167 , PHE A:214 , PHE A:226 , SER A:263 , ALA A:264 , PHE A:270 , ARG A:343 , HIS A:346 , ILE A:349 , TYR A:353 , ILE A:354 , LEU A:384 , LEU A:388 , VAL A:391 , PIM A:502 , NHE A:503 , NHE A:504 , HOH A:619 , HOH A:623 , HOH A:647binding site for residue HEM A 501
2AC2SOFTWAREVAL A:130 , PHE A:163 , SER A:167 , SER A:263 , ALA A:264 , HEM A:501 , NHE A:503binding site for residue PIM A 502
3AC3SOFTWAREGLY A:236 , ALA A:260 , GLY A:261 , ALA A:262 , HEM A:501 , PIM A:502 , NHE A:504binding site for residue NHE A 503
4AC4SOFTWAREARG A:231 , LEU A:384 , PHE A:387 , HEM A:501 , NHE A:503binding site for residue NHE A 504
5AC5SOFTWARESER B:167 , PHE B:214 , PHE B:226 , SER B:263 , ALA B:264 , ARG B:343 , HIS B:346 , ILE B:349 , VAL B:350 , TYR B:353 , ILE B:354 , LEU B:384 , LEU B:388 , VAL B:391 , PIM B:502 , NHE B:503 , NHE B:504 , HOH B:636 , HOH B:639 , HOH B:718binding site for residue HEM B 501
6AC6SOFTWAREVAL B:130 , PHE B:163 , SER B:167 , SER B:263 , ALA B:264 , HEM B:501 , NHE B:503binding site for residue PIM B 502
7AC7SOFTWAREPHE B:226 , LEU B:234 , ALA B:260 , GLY B:261 , ALA B:262 , HEM B:501 , PIM B:502 , NHE B:504binding site for residue NHE B 503
8AC8SOFTWAREARG B:231 , HIS B:287 , LEU B:384 , HEM B:501 , NHE B:503 , HOH B:720binding site for residue NHE B 504

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:308 -B:308

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U74)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U74)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U74)

(-) Exons   (0, 0)

(no "Exon" information available for 4U74)

(-) 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:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh................hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhh.....hhhhhh...eee.......hhh.eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh...ee.............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u74 A  12 SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGASAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPGGTDLMNFLKTVRSTTEKSLLKEG 403
                                    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       271       281       291       301       311       321       331       341       351       361||     388       398     
                                                                                                                                                                                                                                                                                                                                                                                        362|                       
                                                                                                                                                                                                                                                                                                                                                                                         380                       


Chain B from PDB  Type:PROTEIN  Length:374
                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh................hhhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhh.....hhhhhh....ee.......hhh.ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...ee.............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u74 B  11 ISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGASAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQGGTDLMNFLKTVRSTTEKSLLKEG 403
                                    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|      389       399    
                                                                                                                                                                                                                                                                                                                                                                                       360|                       
                                                                                                                                                                                                                                                                                                                                                                                        380
   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 4U74)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U74)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U74)

(-) Gene Ontology  (32, 32)

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
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NHE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PIM  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4u74)
 
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
  4u74
    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
  I23O1_HUMAN | P14902
    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)
  1.13.11.52
    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
  I23O1_HUMAN | P14902
    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
        I23O1_HUMAN | P14902: 2d0t 2d0u 4pk5 4pk6 4u72 5ek2 5ek3 5ek4 5etw 5xe1

(-) Related Entries Specified in the PDB File

2d0t WILD TYPE ENZYME COMPLEXED WITH 4-PHENYLIMIDAZOLE
2d0u WILD TYPE ENZYME COMPLEXED WITH CYANIDE
4u72 A260G MUTANT COMPLEXED WITH 4-PHENYLIMIDAZOLE