SMTL ID : 4gf7.1

Crystal structure of 2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO), unliganded form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 28 residues within 4Å: Chain A: G.18, G.19, G.20, F.21, A.22, H.40, E.41, K.42, S.43, I.53, Y.54, R.106, S.128, E.129, A.130, A.155, D.156, G.157, L.179, R.181, G.287, D.288, P.295, A.298, Q.299, G.300, A.301, G.302 41 PLIP interactions: 41 interactions with chain A Hydrophobic interactions: A:L.179, A:P.295 Hydrogen bonds: A:G.19, A:A.22, A:K.42, A:K.42, A:Y.54, A:Y.54, A:R.106, A:R.106, A:A.130, A:A.130, A:D.156, A:D.288, A:G.300, A:A.301, A:G.302 Water bridges: A:G.19, A:G.19, A:G.20, A:F.21, A:F.21, A:F.21, A:G.23, A:E.41, A:S.43, A:S.43, A:R.47, A:R.47, A:G.157, A:V.158, A:K.161, A:R.181, A:R.181, A:D.288, A:D.288, A:D.288, A:D.288, A:A.289, A:Q.299 pi-Cation interactions: A:R.106 FAD.9: 28 residues within 4Å: Chain B: G.18, G.19, G.20, F.21, A.22, H.40, E.41, K.42, S.43, I.53, Y.54, R.106, S.128, E.129, A.130, A.155, D.156, G.157, L.179, R.181, G.287, D.288, P.295, A.298, Q.299, G.300, A.301, G.302 41 PLIP interactions: 41 interactions with chain B Hydrophobic interactions: B:L.179, B:P.295 Hydrogen bonds: B:G.19, B:A.22, B:K.42, B:K.42, B:Y.54, B:Y.54, B:R.106, B:R.106, B:A.130, B:A.130, B:D.156, B:D.288, B:G.300, B:A.301, B:G.302 Water bridges: B:G.19, B:G.19, B:G.20, B:F.21, B:F.21, B:F.21, B:G.23, B:E.41, B:S.43, B:S.43, B:R.47, B:R.47, B:G.157, B:V.158, B:K.161, B:R.181, B:R.181, B:D.288, B:D.288, B:D.288, B:D.288, B:A.289, B:Q.299 pi-Cation interactions: B:R.106 FAD.17: 28 residues within 4Å: Chain C: G.18, G.19, G.20, F.21, A.22, H.40, E.41, K.42, S.43, I.53, Y.54, R.106, S.128, E.129, A.130, A.155, D.156, G.157, L.179, R.181, G.287, D.288, P.295, A.298, Q.299, G.300, A.301, G.302 41 PLIP interactions: 41 interactions with chain C Hydrophobic interactions: C:L.179, C:P.295 Hydrogen bonds: C:G.19, C:A.22, C:K.42, C:K.42, C:Y.54, C:Y.54, C:R.106, C:R.106, C:E.129, C:A.130, C:A.130, C:D.288, C:G.300, C:A.301, C:G.302 Water bridges: C:G.19, C:G.19, C:G.20, C:F.21, C:F.21, C:F.21, C:G.23, C:E.41, C:S.43, C:S.43, C:R.47, C:R.47, C:G.157, C:V.158, C:K.161, C:R.181, C:R.181, C:Y.223, C:D.288, C:D.288, C:D.288, C:A.289, C:Q.299 pi-Cation interactions: C:R.106 FAD.25: 28 residues within 4Å: Chain D: G.18, G.19, G.20, F.21, A.22, H.40, E.41, K.42, S.43, I.53, Y.54, R.106, S.128, E.129, A.130, A.155, D.156, G.157, L.179, R.181, G.287, D.288, P.295, A.298, Q.299, G.300, A.301, G.302 41 PLIP interactions: 41 interactions with chain D Hydrophobic interactions: D:L.179, D:P.295 Hydrogen bonds: D:G.19, D:A.22, D:K.42, D:K.42, D:Y.54, D:Y.54, D:R.106, D:R.106, D:E.129, D:A.130, D:A.130, D:D.288, D:G.300, D:A.301, D:G.302 Water bridges: D:G.19, D:G.19, D:G.20, D:F.21, D:F.21, D:F.21, D:G.23, D:E.41, D:S.43, D:S.43, D:R.47, D:R.47, D:G.157, D:V.158, D:K.161, D:R.181, D:R.181, D:Y.223, D:D.288, D:D.288, D:D.288, D:A.289, D:Q.299 pi-Cation interactions: D:R.106

4 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 5 residues within 4Å: Chain A: W.173, Y.270, T.272, C.294, A.347 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.175, A:Y.270 BME.10: 5 residues within 4Å: Chain B: W.173, Y.270, T.272, C.294, A.347 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.175, B:Y.270 BME.18: 5 residues within 4Å: Chain C: W.173, Y.270, T.272, C.294, A.347 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.175, C:Y.270 BME.26: 5 residues within 4Å: Chain D: W.173, Y.270, T.272, C.294, A.347 2 PLIP interactions: 2 interactions with chain D Water bridges: D:S.175, D:Y.270

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: L.73, Q.74, G.75, S.76, R.102 Chain B: N.97, P.378 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: K.169, D.171, K.274, D.276 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: E.364, R.367, Y.375 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: R.331, I.335, R.373, Y.375 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: E.94, N.356, T.359, P.360 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain A: N.97, P.378 Chain B: L.73, Q.74, G.75, S.76, R.102 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: K.169, D.171, K.274, D.276 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain B: E.364, R.367, Y.375 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain B: R.331, I.335, R.373, Y.375 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain B: E.94, N.356, T.359, P.360 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain C: L.73, Q.74, G.75, S.76, R.102 Chain D: N.97, P.378 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain C: K.169, D.171, K.274, D.276 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain C: E.364, R.367, Y.375 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain C: R.331, I.335, R.373, Y.375 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain C: E.94, N.356, T.359, P.360 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain C: N.97, P.378 Chain D: L.73, Q.74, G.75, S.76, R.102 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain D: K.169, D.171, K.274, D.276 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain D: E.364, R.367, Y.375 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain D: R.331, I.335, R.373, Y.375 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain D: E.94, N.356, T.359, P.360 Ligand excluded by PLIP

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 4 residues within 4Å: Chain A: N.88, E.247, P.250 Chain C: V.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.88, A:M.248 PEG.16: 4 residues within 4Å: Chain B: N.88, E.247, P.250 Chain D: V.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.88, B:M.248 PEG.24: 4 residues within 4Å: Chain A: V.91 Chain C: N.88, E.247, P.250 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.88, C:M.248 PEG.32: 4 residues within 4Å: Chain B: V.91 Chain D: N.88, E.247, P.250 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.88, D:M.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobayashi, J. et al., Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase. To be Published

Release Date

2013-08-07

Peptides

2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase

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