SMTL ID : 7cn3.1

2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: H.265, S.302, H.318, D.320 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.265, A:H.318, A:D.320, H2O.1, H2O.3 FE2.4: 4 residues within 4Å: Chain B: H.265, S.302, H.318, D.320 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.265, B:S.302, B:H.318, B:D.320, H2O.9 FE2.6: 5 residues within 4Å: Chain C: H.265, S.302, H.318, D.320 Ligands: G6C.7 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.265, C:S.302, C:D.320, H2O.13, H2O.13 FE2.11: 5 residues within 4Å: Chain D: H.265, S.302, H.318, D.320 Ligands: G6C.12 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.265, D:S.302, D:H.318, D:D.320, H2O.20 FE2.15: 4 residues within 4Å: Chain E: H.265, S.302, H.318, D.320 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.265, E:S.302, E:H.318, E:D.320, H2O.26 FE2.19: 4 residues within 4Å: Chain F: H.265, S.302, H.318, D.320 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.265, F:S.302, F:H.318, F:D.320, H2O.31

2 x D6O: (~{Z})-4-formamido-4-oxidanylidene-but-2-enoic acid(Non-covalent)

D6O.2: 10 residues within 4Å: Chain A: T.73, M.102, H.105, E.177, W.187, H.189, F.194, M.288, M.290, R.293 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.73 Hydrogen bonds: A:H.189, A:D.320 Water bridges: A:D.320 Salt bridges: A:H.105 D6O.5: 9 residues within 4Å: Chain B: M.102, H.105, E.177, H.189, F.194, F.196, M.288, M.290, R.293 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.320 Salt bridges: B:H.105

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: Q.7, M.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.7, A:Q.10 EDO.8: 4 residues within 4Å: Chain C: H.64, P.65, T.66, Y.75 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.66, C:T.66, C:Y.75 EDO.9: 4 residues within 4Å: Chain C: R.158, Y.329, D.331, D.332 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.158, C:R.158, C:Y.329 EDO.13: 5 residues within 4Å: Chain D: H.64, P.65, T.66, Y.75, D.78 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.64, D:T.66, D:T.66, D:D.78 EDO.17: 4 residues within 4Å: Chain E: H.64, P.65, T.66, Y.75 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.66, E:T.66 EDO.18: 3 residues within 4Å: Chain E: I.236, T.237, Y.261 No protein-ligand interaction detected (PLIP) EDO.21: 2 residues within 4Å: Chain F: I.236, Y.261 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:I.239 Water bridges: F:I.239 EDO.22: 4 residues within 4Å: Chain F: H.64, P.65, T.66, Y.75 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:H.64, F:T.66, F:T.66, F:Y.75

4 x G6C: 5-oxidanyl-1H-pyridin-2-one(Non-covalent)

G6C.7: 12 residues within 4Å: Chain C: L.104, H.105, E.177, W.187, H.189, F.194, M.288, M.290, R.293, H.318, D.320 Ligands: FE2.6 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.104 Hydrogen bonds: C:E.177, C:H.189 G6C.12: 12 residues within 4Å: Chain D: L.104, H.105, E.177, W.187, H.189, F.194, H.265, M.290, R.293, H.318, D.320 Ligands: FE2.11 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.104 Hydrogen bonds: D:E.177 Water bridges: D:H.105, D:S.302 G6C.16: 11 residues within 4Å: Chain E: L.104, H.105, E.177, W.187, H.189, F.194, M.288, M.290, R.293, H.318, D.320 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.177 G6C.20: 10 residues within 4Å: Chain F: L.104, H.105, E.177, W.187, H.189, F.194, M.290, R.293, H.318, D.320 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.104 Hydrogen bonds: F:H.105, F:E.177, F:H.189

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 3 residues within 4Å: Chain C: K.253, N.256, Y.261 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.261 Water bridges: C:K.253, C:D.257 PGE.14: 6 residues within 4Å: Chain D: I.236, T.237, K.253, N.256, D.257, Y.261 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.257 Water bridges: D:K.253, D:D.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, G.Q. et al., 2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid. Nat Commun (2020)

Release Date

2020-12-16

Peptides

2,5-dihydroxypyridine 5,6-dioxygenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

2,5-dihydroxypyridine 5,6-dioxygenase

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