SMTL ID : 3zds.1 (4 other biounits)

Structure of homogentisate 1,2-dioxygenase in complex with reaction intermediates of homogentisate with oxygen.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

6 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: H.331, E.337, H.367 Ligands: M8O.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.331, A:E.337, A:E.337, A:H.367, H2O.18 FE.3: 4 residues within 4Å: Chain B: H.331, E.337, H.367 Ligands: OMD.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.331, B:E.337, B:E.337, B:H.367, H2O.38 FE.6: 5 residues within 4Å: Chain C: H.331, E.337, H.367 Ligands: OXY.5, HQ9.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.331, C:E.337, C:E.337, C:H.367 FE.8: 4 residues within 4Å: Chain D: H.331, E.337, H.367 Ligands: OMD.9 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.331, D:E.337, D:E.337, D:H.367, H2O.77 FE.10: 4 residues within 4Å: Chain E: H.331, E.337, H.367 Ligands: OMD.11 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.331, E:E.337, E:E.337, E:H.367, H2O.96 FE.13: 4 residues within 4Å: Chain F: H.331, E.337, H.367 Ligands: OMD.14 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.331, F:E.337, F:E.337, F:H.367, H2O.115

1 x M8O: 4-Maleylacetoacetic acid(Non-covalent)

M8O.2: 14 residues within 4Å: Chain A: H.288, P.291, F.314, P.328, W.329, H.331, E.337, M.339, Y.346, A.348, H.367, G.368, M.394 Ligands: FE.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.291, A:F.314, A:P.328, A:P.328, A:W.329 Hydrogen bonds: A:E.337 Salt bridges: A:H.331, A:K.349, A:H.367

4 x OMD: 2-(3,6-DIHYDROXYPHENYL)ACETIC ACID(Non-covalent)

OMD.4: 13 residues within 4Å: Chain B: H.288, P.291, F.314, P.328, W.329, H.331, E.337, M.339, Y.346, A.348, H.367, M.394 Ligands: FE.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.314, B:P.328, B:P.328 Hydrogen bonds: B:Y.346 Salt bridges: B:K.349 pi-Stacking: B:W.329 OMD.9: 13 residues within 4Å: Chain D: H.288, P.291, F.314, P.328, W.329, H.331, E.337, M.339, Y.346, A.348, H.367, M.394 Ligands: FE.8 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:P.291, D:P.291, D:F.314, D:P.328, D:P.328, D:W.329 Hydrogen bonds: D:Y.346, D:Y.346 Water bridges: D:H.288 Salt bridges: D:K.349 OMD.11: 13 residues within 4Å: Chain E: H.288, P.291, F.314, P.328, W.329, H.331, E.337, M.339, Y.346, A.348, H.367, M.394 Ligands: FE.10 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:P.291, E:F.314, E:P.328, E:P.328, E:W.329 Hydrogen bonds: E:Y.346, E:Y.346, E:H.361 Water bridges: E:H.288, E:Y.346 OMD.14: 13 residues within 4Å: Chain F: H.288, P.291, F.314, P.328, W.329, H.331, E.337, M.339, Y.346, A.348, H.367, M.394 Ligands: FE.13 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:F.314, F:P.328, F:P.328 Hydrogen bonds: F:Y.346, F:Y.346 Water bridges: F:H.288, F:Y.346, F:K.349, F:K.349, F:H.361 Salt bridges: F:K.349 pi-Stacking: F:W.329

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.5: 7 residues within 4Å: Chain A: F.52 Chain C: P.291, H.331, E.337, M.394 Ligands: FE.6, HQ9.7 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.333

1 x HQ9: 2-(6-oxidanyl-3-oxidanylidene-cyclohexa-1,4-dien-1-yl)ethanoic acid(Non-covalent)

HQ9.7: 14 residues within 4Å: Chain C: H.288, P.291, F.314, P.328, W.329, H.331, E.337, M.339, Y.346, A.348, H.367, M.394 Ligands: OXY.5, FE.6 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:P.291, C:F.314, C:P.328, C:P.328, C:W.329 Water bridges: C:E.337, C:K.349, C:H.361 Salt bridges: C:K.349

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 3 residues within 4Å: Chain E: E.77, R.78, L.79 1 PLIP interactions: 1 interactions with chain E Water bridges: E:A.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeoung, J.-H. et al., Visualizing the Substrate-, Superoxo-, Alkylperoxo- and Product-Bound States at the Non-Heme Fe(II) Site of Homogentisate Dioxygenase. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-07-24

Peptides

HOMOGENTISATE 1,2-DIOXYGENASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

HOMOGENTISATE 1,2-DIOXYGENASE

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