SMTL ID : 4h2r.1

Structure of MHPCO Y270F mutant, 5-hydroxynicotinic acid complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 29 residues within 4Å: Chain A: G.18, G.19, G.20, F.21, A.22, H.40, E.41, K.42, I.53, Y.54, R.106, S.128, E.129, A.130, A.155, D.156, G.157, L.179, R.181, F.270, G.287, D.288, P.295, A.298, Q.299, G.300, A.301, G.302 Ligands: 5HN.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.179, A:F.270, A:F.270, A:P.295 Hydrogen bonds: A:G.19, A:G.20, A:A.22, 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.23, A:G.157, A:V.158, A:A.289, A:Q.299 pi-Cation interactions: A:R.106 FAD.7: 28 residues within 4Å: Chain B: G.18, G.19, G.20, F.21, A.22, H.40, E.41, K.42, F.49, 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 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.179, B:P.295 Hydrogen bonds: B:G.19, B:G.19, B:A.22, B:K.42, B:Y.54, B:Y.54, B:R.106, B:R.106, B:A.130, B:A.130, B:D.288, B:G.300, B:A.301, B:G.302 Water bridges: B:G.20, B:G.23, B:Q.299 pi-Cation interactions: B:K.42, B:R.106, B:R.181 FAD.10: 29 residues within 4Å: Chain C: G.18, G.19, G.20, F.21, A.22, H.40, E.41, K.42, I.53, Y.54, R.106, S.128, E.129, A.130, A.155, D.156, G.157, L.179, R.181, F.270, G.287, D.288, P.295, A.298, Q.299, G.300, A.301, G.302 Ligands: 5HN.12 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:L.179, C:F.270, C:F.270, C:P.295 Hydrogen bonds: C:G.19, C:G.20, C:A.22, C:K.42, C:Y.54, C:Y.54, C:R.106, C:R.106, C:A.130, C:A.130, C:D.288, C:G.300, C:A.301, C:G.302 Water bridges: C:G.23, C:G.157, C:V.158, C:A.289, C:Q.299 pi-Cation interactions: C:R.106 FAD.16: 28 residues within 4Å: Chain D: G.18, G.19, G.20, F.21, A.22, H.40, E.41, K.42, F.49, 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 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:L.179, D:P.295 Hydrogen bonds: D:G.19, D:G.19, D:A.22, D:K.42, D:Y.54, D:Y.54, D:R.106, D:R.106, D:A.130, D:A.130, D:D.156, D:D.288, D:G.300, D:A.301, D:G.302 Water bridges: D:G.20, D:G.23, D:Q.299 pi-Cation interactions: D:K.42, D:R.106, D:R.181

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

BME.2: 5 residues within 4Å: Chain A: S.175, F.270, C.294, A.347, A.348 No protein-ligand interaction detected (PLIP) BME.11: 5 residues within 4Å: Chain C: S.175, F.270, C.294, A.347, A.348 No protein-ligand interaction detected (PLIP)

2 x 5HN: 5-hydroxypyridine-3-carboxylic acid(Non-covalent)

5HN.3: 8 residues within 4Å: Chain A: L.179, R.211, L.213, Y.223, P.295, A.296, A.298 Ligands: FAD.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.213 Hydrogen bonds: A:Y.223, A:Y.223 Salt bridges: A:R.211 5HN.12: 8 residues within 4Å: Chain C: L.179, R.211, L.213, Y.223, P.295, A.296, A.298 Ligands: FAD.10 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.213 Hydrogen bonds: C:Y.223 Salt bridges: C:R.211

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: R.331, I.335, Y.368, R.373, Y.375 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.331, A:Y.368, A:R.373, A:Y.375, A:Y.375 GOL.5: 3 residues within 4Å: Chain A: E.364, R.367, Y.375 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.367, A:R.367 GOL.6: 5 residues within 4Å: Chain A: T.279, R.280, G.281, E.322, V.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.279, A:R.280, A:G.281, A:G.281 GOL.8: 7 residues within 4Å: Chain A: R.61, E.64, L.69 Chain B: H.57, R.61, S.376, W.377 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.376, B:S.376 Water bridges: B:R.61 GOL.9: 3 residues within 4Å: Chain B: R.331, Y.368, R.373 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.331, B:Y.368, B:R.373 GOL.13: 5 residues within 4Å: Chain C: R.331, I.335, Y.368, R.373, Y.375 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.331, C:R.373, C:Y.375 GOL.14: 3 residues within 4Å: Chain C: E.364, R.367, Y.375 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.367, C:R.367 GOL.15: 5 residues within 4Å: Chain C: T.279, R.280, G.281, E.322, V.326 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.279, C:R.280, C:G.281, C:G.281 GOL.17: 7 residues within 4Å: Chain C: R.61, E.64, L.69 Chain D: H.57, R.61, S.376, W.377 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.376, D:S.376 Water bridges: D:R.61 GOL.18: 3 residues within 4Å: Chain D: R.331, Y.368, R.373 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.331, D:Y.368, D:Y.368, D:R.373

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

2013-09-18

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

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

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