SMTL ID : 5hxi.1

2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5HN bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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, 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 Ligands: 5HN.3 36 PLIP interactions: 36 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.20, A:F.21, A:F.21, A:G.23, A:E.41, A:S.43, 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.11: 29 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 Ligands: 5HN.13 36 PLIP interactions: 36 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.20, B:F.21, B:F.21, B:G.23, B:E.41, B:S.43, 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.21: 29 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 Ligands: 5HN.23 37 PLIP interactions: 37 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.20, C:F.21, C:F.21, C:G.23, C:E.41, C:S.43, 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:D.288, C:A.289, C:Q.299 pi-Cation interactions: C:R.106 FAD.31: 29 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 Ligands: 5HN.33 37 PLIP interactions: 37 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.20, D:F.21, D:F.21, D:G.23, D:E.41, D:S.43, 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:D.288, D:A.289, D:Q.299 pi-Cation interactions: D:R.106

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

BME.2: 4 residues within 4Å: Chain A: W.173, Y.270, C.294, A.347 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.347, A:R.350 BME.12: 4 residues within 4Å: Chain B: W.173, Y.270, C.294, A.347 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.347, B:R.350 BME.22: 4 residues within 4Å: Chain C: W.173, Y.270, C.294, A.347 2 PLIP interactions: 2 interactions with chain C Water bridges: C:A.347, C:R.350 BME.32: 4 residues within 4Å: Chain D: W.173, Y.270, C.294, A.347 2 PLIP interactions: 2 interactions with chain D Water bridges: D:A.347, D:R.350

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

5HN.3: 9 residues within 4Å: Chain A: R.211, L.213, Y.223, M.227, Y.270, P.295, A.296, L.352 Ligands: FAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.295 Hydrogen bonds: A:Y.270 Water bridges: A:R.211, A:R.211, A:Y.223, A:A.296, A:A.296 Salt bridges: A:R.211 5HN.13: 9 residues within 4Å: Chain B: R.211, L.213, Y.223, M.227, Y.270, P.295, A.296, L.352 Ligands: FAD.11 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.295 Hydrogen bonds: B:Y.270 Water bridges: B:R.211, B:R.211, B:Y.223, B:A.296, B:A.296 Salt bridges: B:R.211 5HN.23: 9 residues within 4Å: Chain C: R.211, L.213, Y.223, M.227, Y.270, P.295, A.296, L.352 Ligands: FAD.21 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:P.295 Hydrogen bonds: C:Y.223, C:Y.270, C:Y.270 Water bridges: C:R.211, C:R.211, C:Y.223, C:A.296, C:A.296 Salt bridges: C:R.211 5HN.33: 9 residues within 4Å: Chain D: R.211, L.213, Y.223, M.227, Y.270, P.295, A.296, L.352 Ligands: FAD.31 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:P.295 Hydrogen bonds: D:Y.223, D:Y.270, D:Y.270 Water bridges: D:R.211, D:R.211, D:Y.223, D:A.296, D:A.296 Salt bridges: D:R.211

8 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: M.293, Q.299, C.339, Q.340 Ligands: NA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.339 Water bridges: A:S.343 NA.5: 6 residues within 4Å: Chain A: M.293, Q.299, C.303, C.339, A.365 Ligands: NA.4 No protein-ligand interaction detected (PLIP) NA.14: 5 residues within 4Å: Chain B: M.293, Q.299, C.339, Q.340 Ligands: NA.15 2 PLIP interactions: 2 interactions with chain B Water bridges: B:C.294, B:S.343 NA.15: 6 residues within 4Å: Chain B: M.293, Q.299, C.303, C.339, A.365 Ligands: NA.14 No protein-ligand interaction detected (PLIP) NA.24: 5 residues within 4Å: Chain C: M.293, Q.299, C.339, Q.340 Ligands: NA.25 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:C.339 Water bridges: C:S.343 NA.25: 6 residues within 4Å: Chain C: M.293, Q.299, C.303, C.339, A.365 Ligands: NA.24 No protein-ligand interaction detected (PLIP) NA.34: 5 residues within 4Å: Chain D: M.293, Q.299, C.339, Q.340 Ligands: NA.35 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:C.339 Water bridges: D:S.343 NA.35: 6 residues within 4Å: Chain D: M.293, Q.299, C.303, C.339, A.365 Ligands: NA.34 No protein-ligand interaction detected (PLIP)

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: N.97, P.378, Q.379 Chain B: L.73, Q.74, G.75, S.76, N.218 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: E.364, R.367, Y.375 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: K.169, Q.170, D.171, K.274, D.276 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: H.57, R.61, D.369, R.372, S.376, W.377 Chain B: E.64, L.69 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain A: L.73, Q.74, G.75, S.76, N.218 Chain B: N.97, P.378, Q.379 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain B: E.364, R.367, Y.375 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: K.169, Q.170, D.171, K.274, D.276 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain A: E.64, L.69 Chain B: H.57, R.61, D.369, R.372, S.376, W.377 Ligand excluded by PLIP GOL.26: 8 residues within 4Å: Chain C: N.97, P.378, Q.379 Chain D: L.73, Q.74, G.75, S.76, N.218 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain C: E.364, R.367, Y.375 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain C: K.169, Q.170, D.171, K.274, D.276 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain C: H.57, R.61, D.369, R.372, S.376, W.377 Chain D: E.64, L.69 Ligand excluded by PLIP GOL.36: 8 residues within 4Å: Chain C: L.73, Q.74, G.75, S.76, N.218 Chain D: N.97, P.378, Q.379 Ligand excluded by PLIP GOL.37: 3 residues within 4Å: Chain D: E.364, R.367, Y.375 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain D: K.169, Q.170, D.171, K.274, D.276 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain C: E.64, L.69 Chain D: H.57, R.61, D.369, R.372, S.376, W.377 Ligand excluded by PLIP

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

PEG.10: 5 residues within 4Å: Chain A: N.88, W.206, P.207, E.247 Chain C: V.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.88 Water bridges: A:W.206 PEG.20: 5 residues within 4Å: Chain B: N.88, W.206, P.207, E.247 Chain D: V.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.88 Water bridges: B:W.206 PEG.30: 5 residues within 4Å: Chain A: V.91 Chain C: N.88, W.206, P.207, E.247 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.88 Water bridges: C:W.206 PEG.40: 5 residues within 4Å: Chain B: V.91 Chain D: N.88, W.206, P.207, E.247 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.88 Water bridges: D:W.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobayashi, J. et al., Role of the Tyr270 residue in 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti. J. Biosci. Bioeng. (2017)

Release Date

2016-10-12

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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