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(-) Description

Title :  CRYSTAL STRUCTURE OF 4-PHENYLIMIDAZOLE BOUND FORM OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE
 
Authors :  H. Sugimoto, S. Oda, T. Otsuki, T. Hino, T. Yoshida, Y. Shiro, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  08 Aug 05  (Deposition) - 31 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Helix Bundle, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Sugimoto, S. Oda, T. Otsuki, T. Hino, T. Yoshida, Y. Shiro
Crystal Structure Of Human Indoleamine 2, 3-Dioxygenase: Catalytic Mechanism Of O2 Incorporation By A Heme-Containing Dioxygenase.
Proc. Natl. Acad. Sci. Usa V. 103 2611 2006
PubMed-ID: 16477023  |  Reference-DOI: 10.1073/PNAS.0508996103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INDOLEAMINE 2,3-DIOXYGENASE
    ChainsA, B
    EC Number1.13.11.42
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-15B
    Expression System StrainBL21(DE3) CODONPLUS-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIDO, 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
1AC1SOFTWAREPHE A:163 , SER A:167 , PHE A:214 , PHE A:226 , SER A:263 , ALA A:264 , ARG A:343 , HIS A:346 , ILE A:349 , VAL A:350 , LEU A:384 , VAL A:391 , PIM A:501 , NHE A:502 , NHE A:503 , HOH A:506 , HOH A:514BINDING SITE FOR RESIDUE HEM A 404
2AC2SOFTWAREPHE B:163 , SER B:167 , PHE B:214 , ILE B:217 , PHE B:226 , SER B:263 , ALA B:264 , ARG B:343 , HIS B:346 , ILE B:349 , VAL B:350 , ILE B:354 , LEU B:384 , VAL B:391 , PIM B:1501 , NHE B:1502 , NHE B:1503 , HOH B:1509BINDING SITE FOR RESIDUE HEM B 404
3AC3SOFTWAREVAL A:130 , PHE A:163 , PHE A:164 , SER A:167 , SER A:263 , ALA A:264 , HEM A:404 , NHE A:502BINDING SITE FOR RESIDUE PIM A 501
4AC4SOFTWARELEU A:234 , GLY A:236 , ALA A:260 , GLY A:261 , GLY A:262 , HEM A:404 , PIM A:501 , NHE A:503BINDING SITE FOR RESIDUE NHE A 502
5AC5SOFTWARELEU A:384 , HEM A:404 , NHE A:502BINDING SITE FOR RESIDUE NHE A 503
6AC6SOFTWAREVAL B:130 , PHE B:163 , SER B:167 , SER B:263 , ALA B:264 , HEM B:404 , NHE B:1502BINDING SITE FOR RESIDUE PIM B 1501
7AC7SOFTWARELEU B:234 , GLY B:236 , ALA B:260 , GLY B:261 , GLY B:262 , HEM B:404 , PIM B:1501BINDING SITE FOR RESIDUE NHE B 1502
8AC8SOFTWAREHIS B:287 , LEU B:384 , HEM B:404BINDING SITE FOR RESIDUE NHE B 1503

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D0T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D0T)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDO_1PS00876 Indoleamine 2,3-dioxygenase signature 1.I23O1_HUMAN261-271
 
  2A:261-271
B:261-271
2IDO_2PS00877 Indoleamine 2,3-dioxygenase signature 2.I23O1_HUMAN291-304
 
  2A:291-304
B:291-304
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDO_1PS00876 Indoleamine 2,3-dioxygenase signature 1.I23O1_HUMAN261-271
 
  1A:261-271
-
2IDO_2PS00877 Indoleamine 2,3-dioxygenase signature 2.I23O1_HUMAN291-304
 
  1A:291-304
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDO_1PS00876 Indoleamine 2,3-dioxygenase signature 1.I23O1_HUMAN261-271
 
  1-
B:261-271
2IDO_2PS00877 Indoleamine 2,3-dioxygenase signature 2.I23O1_HUMAN291-304
 
  1-
B:291-304

(-) Exons   (0, 0)

(no "Exon" information available for 2D0T)

(-) 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:373
 aligned with I23O1_HUMAN | P14902 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:392
                                    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       371       381       391       401  
          I23O1_HUMAN    12 SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG 403
               SCOP domains d2d0ta1 A:12-403 Indoleamine 2,3-dioxygenase                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhh.....hhhhhh...eee.......hhh.eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh...ee.............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-------------------.hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDO_1      -------------------IDO_2         --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d0t A  12 SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQ-------------------GGTDLMNFLKTVRSTTEKSLLKEG 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        |-         -       381       391       401  
                                                                                                                                                                                                                                                                                                                                                                                      360                 380                       

Chain B from PDB  Type:PROTEIN  Length:374
 aligned with I23O1_HUMAN | P14902 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:393
                                    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       380       390       400   
          I23O1_HUMAN    11 ISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG 403
               SCOP domains d2d0tb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhh.....hhhhhh....ee.......hhh.ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh...ee.............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-------------------.hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDO_1      -------------------IDO_2         --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d0t B  11 ISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQ-------------------GGTDLMNFLKTVRSTTEKSLLKEG 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         -       380       390       400   
                                                                                                                                                                                                                                                                                                                                                                                       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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D0T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D0T)

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (I23O1_HUMAN | P14902)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0033754    indoleamine 2,3-dioxygenase activity    Catalysis of the reaction: tryptophan + O2 = N-formylkynurenine. The product of the reaction depends on the substrate; D-tryptophan produces N-formyl-D-kynurenine, and L-tryptophan produces N-formyl-L-kynurenine.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004833    tryptophan 2,3-dioxygenase activity    Catalysis of the reaction: L-tryptophan + O2 = N-formyl-L-kynurenine.
biological process
    GO:0002534    cytokine production involved in inflammatory response    The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0034276    kynurenic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of kynurenic acid, 4-hydroxyquinoline-2-carboxylic acid.
    GO:0033555    multicellular organismal response to stress    Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0070233    negative regulation of T cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of T cell death by apoptotic process.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0032693    negative regulation of interleukin-10 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-10 production.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0070234    positive regulation of T cell apoptotic process    Any process that activates or increases the frequency, rate or extent of T cell death by apoptotic process.
    GO:0002666    positive regulation of T cell tolerance induction    Any process that activates or increases the frequency, rate, or extent of T cell tolerance induction.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0002678    positive regulation of chronic inflammatory response    Any process that activates or increases the frequency, rate, or extent of a chronic inflammatory response.
    GO:0032735    positive regulation of interleukin-12 production    Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
    GO:0002830    positive regulation of type 2 immune response    Any process that activates or increases the frequency, rate, or extent of a type 2 immune response.
    GO:0046006    regulation of activated T cell proliferation    Any process that modulates the frequency, rate or extent of activated T cell proliferation.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0036269    swimming behavior    The response to external or internal stimuli that results in the locomotory process of swimming. Swimming is the self-propelled movement of an organism through the water.
    GO:0006569    tryptophan catabolic process    The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
    GO:0019441    tryptophan catabolic process to kynurenine    The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including kynurenine.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030485    smooth muscle contractile fiber    The contractile fiber of smooth muscle cells.
    GO:0032421    stereocilium bundle    A bundle of cross-linked stereocilia, arranged around a kinocilium on the apical surface of a sensory hair cell (e.g. a neuromast, auditory or vestibular hair cell). Stereocilium bundles act as mechanosensory organelles by responding to fluid motion or fluid pressure changes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        I23O1_HUMAN | P149022d0u 4pk5 4pk6 4u72 4u74 5ek2 5ek3 5ek4 5etw 5xe1

(-) Related Entries Specified in the PDB File

2d0u LIGAND WAS EXCHANGED FROM PHENYLIMIDAZOLE TO CYANIDE RELATED ID: MY_001000021.1 RELATED DB: TARGETDB