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(-) Description

Title :  CRYSTAL STRUCTURE OF 4-PHENYLIMIDAZOLE BOUND FORM OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE (A260G 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 :  2.00
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
    Fragment: INDOLEAMINE 2,3-DIOXYGENASE
    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 , VAL A:350 , TYR A:353 , LEU A:384 , LEU A:388 , VAL A:391 , PIM A:502 , NHE A:503 , NHE A:504 , HOH A:619 , HOH A:629 , HOH A:672binding 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
3AC3SOFTWAREPHE A:163 , PHE A:226 , SER A:235 , GLY A:236 , GLY A:260 , GLY A:261 , GLY A:262 , HEM A:501 , PIM A:502 , NHE A:504 , HOH A:684binding site for residue NHE A 503
4AC4SOFTWAREARG A:231 , LYS A:238 , GLY A:260 , HIS A:287 , PHE A:291 , HEM A:501 , NHE A:503binding site for residue NHE A 504
5AC5SOFTWAREPHE B:163 , SER B:167 , PHE B:214 , PHE B:226 , SER B:263 , ALA B:264 , PHE B:270 , 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:632 , HOH B:635 , HOH B:686binding 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:163 , PHE B:226 , SER B:235 , GLY B:236 , GLY B:260 , GLY B:261 , GLY B:262 , HEM B:501 , PIM B:502 , NHE B:504 , HOH B:671binding site for residue NHE B 503
8AC8SOFTWAREARG B:231 , LYS B:238 , GLY B:260 , HIS B:287 , PHE B:291 , LEU B:384 , PHE B:387 , HEM B:501 , NHE B:503 , HOH B:652binding 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 4U72)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U72)

(-) Exons   (0, 0)

(no "Exon" information available for 4U72)

(-) 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.hhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhh.....hhhhhh....ee.......hhh.ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh...ee.............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u72 A  12 SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFGGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPGGTDLMNFLKTVRSTTEKSLLKEG 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.hhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhh.....hhhhhh....ee.......hhh.ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...ee.............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u72 B  11 ISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFGGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQGGTDLMNFLKTVRSTTEKSLLKEG 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 4U72)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U72)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U72)

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        I23O1_HUMAN | P14902: 2d0t 2d0u 4pk5 4pk6 4u74 5ek2 5ek3 5ek4 5etw 5xe1

(-) Related Entries Specified in the PDB File

2d0t WILD TYPE ENZYME