SMTL ID : 4aq6.2 (1 other biounit)

substrate bound homogentisate 1,2-dioxygenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 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: OMD.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.13 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.27 FE.5: 4 residues within 4Å: Chain C: H.331, E.337, H.367 Ligands: OMD.6 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.331, C:E.337, C:E.337, C:H.367, H2O.40 FE.7: 4 residues within 4Å: Chain D: H.331, E.337, H.367 Ligands: OMD.8 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.53 FE.9: 4 residues within 4Å: Chain E: H.331, E.337, H.367 Ligands: OMD.10 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.67 FE.12: 4 residues within 4Å: Chain F: H.331, E.337, H.367 Ligands: OMD.13 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.80

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

OMD.2: 13 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, M.394 Ligands: FE.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.291, A:F.314, A:P.328, A:P.328 Hydrogen bonds: A:Y.346 Water bridges: A:K.349 Salt bridges: A:K.349 pi-Stacking: A:W.329 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 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:P.291, B:F.314, B:P.328, B:P.328, B:W.329 Hydrogen bonds: B:Y.346 Water bridges: B:H.288, B:Y.346, B:G.368 Salt bridges: B:K.349 OMD.6: 13 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: FE.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.314, C:P.328, C:W.329 Hydrogen bonds: C:Y.346 Water bridges: C:H.288, C:Y.346 Salt bridges: C:K.349 OMD.8: 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.7 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.314, D:P.328, D:P.328, D:W.329 Hydrogen bonds: D:Y.346, D:Y.346 Water bridges: D:H.361 Salt bridges: D:K.349 OMD.10: 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.9 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: 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:Y.346 Salt bridges: E:K.349 OMD.13: 13 residues within 4Å: Chain F: H.288, P.291, P.328, W.329, H.331, E.337, M.339, Y.346, A.348, H.361, H.367, M.394 Ligands: FE.12 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:P.291, F:P.328, F:W.329 Hydrogen bonds: F:Y.346, F:Y.346, F:H.361 Water bridges: F:H.288, F:Y.346 Salt bridges: F:K.349

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.11: 3 residues within 4Å: Chain E: E.141, R.142, Q.240 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.141, E:R.142 Water bridges: E:R.138, E:R.138, E:Q.240

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

2013-04-24

Peptides

HOMOGENTISATE 1,2-DIOXYGENASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

HOMOGENTISATE 1,2-DIOXYGENASE

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