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(-) Description

Title :  CRYSTAL STRUCTURE OF THE INDOLEAMINE 2,3-DIOXYGENAGSE 1 (IDO1) COMPLEXED WITH AMG-1
 
Authors :  T. Kohno, S. Tojo, T. Ishii
Date :  13 May 14  (Deposition) - 03 Sep 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Indoleamine 2, 3-Dioxygenagse 1, Induced Fit, Structure Based Drug Discovery, Imidazothiazole, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Tojo, T. Kohno, T. Tanaka, S. Kamioka, Y. Ota, T. Ishii, K. Kamimoto, S. Asano, Y. Isobe
Crystal Structures And Structure-Activity Relationships Of Imidazothiazole Derivatives As Ido1 Inhibitors.
Acs Med. Chem. Lett. V. 5 1119 2014
PubMed-ID: 25313323  |  Reference-DOI: 10.1021/ML500247W

(-) Compounds

Molecule 1 - INDOLEAMINE 2,3-DIOXYGENASE 1
    ChainsA, B
    EC Number1.13.11.52
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneIDO1, IDO, INDO
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIDO-1,INDOLEAMINE-PYRROLE 2,3-DIOXYGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PKJ2Ligand/IonN-(1,3-BENZODIOXOL-5-YL)-2-{[5-(4-METHYLPHENYL)[1,3]THIAZOLO[2,3-C][1,2,4]TRIAZOL-3-YL]SULFANYL}ACETAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:163 , PHE A:214 , PHE A:226 , SER A:263 , ALA A:264 , GLY A:265 , PHE A:270 , ARG A:343 , HIS A:346 , ILE A:349 , ILE A:354 , PHE A:387 , VAL A:391 , PKJ A:502binding site for residue HEM A 501
2AC2SOFTWAREVAL A:125 , TYR A:126 , CYS A:129 , PHE A:163 , SER A:167 , PHE A:226 , PHE A:227 , ARG A:231 , GLY A:262 , SER A:263 , ALA A:264 , ILE A:354 , LEU A:384 , HEM A:501binding site for residue PKJ A 502
3AC3SOFTWAREPHE B:163 , SER B:167 , PHE B:214 , PHE B:226 , SER B:263 , ALA B:264 , GLY B:265 , PHE B:270 , PHE B:291 , ARG B:343 , HIS B:346 , ILE B:349 , VAL B:350 , PHE B:387 , VAL B:391 , PKJ B:502binding site for residue HEM B 501
4AC4SOFTWARETYR B:126 , CYS B:129 , PHE B:163 , SER B:167 , PHE B:227 , ARG B:231 , GLY B:262 , SER B:263 , ALA B:264 , ILE B:354 , LEU B:384 , HEM B:501 , HOH B:603binding site for residue PKJ B 502

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PK5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PK5)

(-) Exons   (0, 0)

(no "Exon" information available for 4PK5)

(-) 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:373
                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhh......hhhhhh...eee.......hhh.eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..eee......ee.....hhhhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pk5 A  12 SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQGGTDLMNFLKTVRSTTEKSLLKEG 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       380       390       400   
                                                                                                                                                                                                                                                                                                                                                                                      360|                       
                                                                                                                                                                                                                                                                                                                                                                                       380                       

Chain B from PDB  Type:PROTEIN  Length:373
                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhh.....hhhhhh....ee...........ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eee......ee.....hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pk5 B  12 SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQGGTDLMNFLKTVRSTTEKSLLKEG 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       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  (0, 0)

(no "SCOP Domain" information available for 4PK5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PK5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PK5)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        I23O1_HUMAN | P149022d0t 2d0u 4pk6 4u72 4u74 5ek2 5ek3 5ek4 5etw 5xe1

(-) Related Entries Specified in the PDB File

4pk6