SMTL ID : 4h2p.1

Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 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, I.53, Y.54, R.106, S.128, E.129, A.130, A.155, D.156, G.157, L.179, R.181, Y.270, G.287, D.288, P.295, A.298, Q.299, G.300, A.301, G.302 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:L.179, A:Y.270, A:P.295 Hydrogen bonds: A:G.19, A:G.19, 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.20, A:F.21, A:F.21, A:G.23, A:S.43, A:S.43, A:S.43, A:G.157, A:V.158, A:K.161, A:R.181, A:R.181, A:Y.223, A:D.288, A:D.288, A:D.288, A:A.289, A:Q.299 pi-Cation interactions: A:R.106 FAD.20: 27 residues within 4Å: Chain B: 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, G.287, D.288, P.295, A.298, Q.299, G.300, A.301, G.302 35 PLIP interactions: 35 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:V.286, B:D.288, B:G.300, B:A.301, B:G.302 Water bridges: B:G.20, B:G.23, B:S.43, B:S.43, B:S.43, B:E.129, 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.50: 27 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, G.287, D.288, P.295, A.298, Q.299, G.300, A.301, G.302 37 PLIP interactions: 37 interactions with chain C Hydrophobic interactions: C:L.179, C:P.295 Hydrogen bonds: C:G.19, C:G.19, C:A.22, 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.156, C:D.288, C:G.300, C:A.301, C:G.302 Water bridges: C:G.20, C:F.21, C:G.23, C:K.42, C:S.43, C:S.43, 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:A.289, C:Q.299 pi-Cation interactions: C:R.106 FAD.74: 27 residues within 4Å: Chain D: 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, G.287, D.288, P.295, A.298, Q.299, G.300, A.301, G.302 35 PLIP interactions: 35 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.288, D:G.300, D:A.301, D:G.302 Water bridges: D:G.20, D:F.21, D:G.23, D:K.42, D:S.43, D:S.43, D:R.47, D:G.157, D:V.158, D:K.161, D:R.181, D:R.181, 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: 6 residues within 4Å: Chain A: W.173, Y.270, T.272, C.294, A.347 Ligands: SO4.4 No protein-ligand interaction detected (PLIP) BME.21: 6 residues within 4Å: Chain B: W.173, Y.270, C.294, A.347 Ligands: SO4.23, PEG.42 No protein-ligand interaction detected (PLIP) BME.51: 6 residues within 4Å: Chain C: W.173, Y.270, T.272, C.294, A.347 Ligands: EDO.58 No protein-ligand interaction detected (PLIP) BME.75: 7 residues within 4Å: Chain D: W.173, Y.270, T.272, C.294, P.295, A.347 Ligands: EDO.86 No protein-ligand interaction detected (PLIP)

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: R.47, A.48, F.49, G.50, A.51, R.266 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.47, A:G.50, A:A.51 Water bridges: A:G.50, A:T.264, A:R.266, A:R.266, A:R.266 Salt bridges: A:R.266 SO4.4: 6 residues within 4Å: Chain A: W.173, S.175, K.176, D.177, R.350 Ligands: BME.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.176, A:D.177, A:D.177 Water bridges: A:K.176 Salt bridges: A:K.176, A:R.350 SO4.22: 4 residues within 4Å: Chain B: F.49, G.50, A.51, R.266 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.50, B:A.51 Water bridges: B:R.47, B:I.183, B:T.264, B:R.266, B:R.266 Salt bridges: B:R.266 SO4.23: 7 residues within 4Å: Chain B: W.173, S.175, K.176, D.177, R.350 Ligands: BME.21, PEG.42 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.176, B:D.177, B:D.177, B:D.177 Salt bridges: B:R.350 SO4.24: 2 residues within 4Å: Chain B: R.280, G.281 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.281 SO4.52: 6 residues within 4Å: Chain C: R.47, A.48, F.49, G.50, A.51, R.266 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.47, C:G.50, C:A.51 Water bridges: C:R.266, C:R.266 Salt bridges: C:R.266 SO4.53: 5 residues within 4Å: Chain C: F.168, K.169, D.276, S.277, R.280 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.169, C:S.277 Water bridges: C:D.276 Salt bridges: C:K.169, C:R.280 SO4.54: 2 residues within 4Å: Chain C: R.280, G.281 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.281 SO4.76: 4 residues within 4Å: Chain D: F.49, G.50, A.51, R.266 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.50, D:A.51 Water bridges: D:I.183, D:R.266, D:R.266 Salt bridges: D:R.266 SO4.77: 2 residues within 4Å: Chain D: S.43, S.44 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.44, D:S.44 Water bridges: D:S.43 SO4.78: 6 residues within 4Å: Chain D: G.167, F.168, K.169, D.276, S.277, R.280 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.169, D:S.277 Water bridges: D:D.276 Salt bridges: D:R.280 SO4.79: 2 residues within 4Å: Chain D: R.280, G.281 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.281

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

EDO.5: 6 residues within 4Å: Chain A: N.127, S.128, E.129, L.141, Q.142, T.143 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: F.205, N.349 Ligands: EDO.65 Ligand excluded by PLIP EDO.7: 1 residues within 4Å: Chain A: F.49 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: K.261, L.262, K.263, T.264 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: S.43, S.44 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: F.168, K.169, D.276, S.277, R.280 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: T.143, E.145 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: R.116, L.120 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: I.183, V.184, P.185, N.220, E.221 Ligands: PEG.40 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain B: F.205, N.349 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: Q.170, D.171, K.274, L.275, D.276 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain B: R.186, M.187, K.188, K.189, E.190, E.219 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: P.185, M.187, E.258 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: W.85, N.88, F.251 Chain D: K.89 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: N.127, S.128, E.129, L.141, Q.142, T.143 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain A: R.372, V.374 Chain B: D.70 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain B: N.356, F.358, T.359 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain B: K.261, L.262, K.263, T.264 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain B: F.168, K.169, D.276, S.277, R.280 Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Chain B: T.143, E.145 Ligand excluded by PLIP EDO.37: 2 residues within 4Å: Chain B: S.43, S.44 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain B: R.116, L.120 Ligand excluded by PLIP EDO.39: 1 residues within 4Å: Chain B: K.42 Ligand excluded by PLIP EDO.55: 1 residues within 4Å: Chain C: R.116 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain C: P.185, M.187, E.258 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain A: K.89 Chain C: W.85, N.88, F.251 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain C: G.344, A.348 Ligands: BME.51 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain C: I.335, Y.368, R.373, Y.375 Ligand excluded by PLIP EDO.60: 2 residues within 4Å: Chain C: R.367 Ligands: EDO.61 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain C: E.364, R.367, Y.375 Ligands: EDO.60 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain C: K.42, E.129, K.161 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain C: D.164, S.165, I.166 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain C: K.261, L.262, K.263, T.264 Ligand excluded by PLIP EDO.65: 2 residues within 4Å: Chain C: W.206 Ligands: EDO.6 Ligand excluded by PLIP EDO.66: 2 residues within 4Å: Chain C: S.43, S.44 Ligand excluded by PLIP EDO.67: 5 residues within 4Å: Chain C: R.186, M.187, K.188, K.189, E.190 Ligand excluded by PLIP EDO.80: 1 residues within 4Å: Chain D: R.13 Ligand excluded by PLIP EDO.81: 4 residues within 4Å: Chain D: R.13, E.148, A.149, D.150 Ligand excluded by PLIP EDO.82: 2 residues within 4Å: Chain D: R.116, L.120 Ligand excluded by PLIP EDO.83: 3 residues within 4Å: Chain D: R.118, A.119, G.121 Ligand excluded by PLIP EDO.84: 4 residues within 4Å: Chain B: K.89 Chain D: W.85, N.88, F.251 Ligand excluded by PLIP EDO.85: 1 residues within 4Å: Chain D: F.49 Ligand excluded by PLIP EDO.86: 5 residues within 4Å: Chain D: W.173, C.294, G.344, A.348 Ligands: BME.75 Ligand excluded by PLIP EDO.87: 2 residues within 4Å: Chain D: V.209, P.229 Ligand excluded by PLIP EDO.88: 3 residues within 4Å: Chain D: Y.368, R.373, Y.375 Ligand excluded by PLIP EDO.89: 2 residues within 4Å: Chain D: R.367 Ligands: EDO.90 Ligand excluded by PLIP EDO.90: 5 residues within 4Å: Chain D: R.338, E.364, R.367, Y.375 Ligands: EDO.89 Ligand excluded by PLIP EDO.91: 2 residues within 4Å: Chain D: K.42, K.161 Ligand excluded by PLIP EDO.92: 3 residues within 4Å: Chain D: S.165, I.166, G.167 Ligand excluded by PLIP EDO.93: 3 residues within 4Å: Chain D: G.159, D.164, R.172 Ligand excluded by PLIP EDO.94: 5 residues within 4Å: Chain D: R.186, M.187, K.188, K.189, E.190 Ligand excluded by PLIP

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

PEG.13: 4 residues within 4Å: Chain A: N.218, N.220, E.221 Ligands: PEG.15 Ligand excluded by PLIP PEG.14: 2 residues within 4Å: Chain A: K.42, K.161 Ligand excluded by PLIP PEG.15: 5 residues within 4Å: Chain A: I.183, V.184, P.185, N.220 Ligands: PEG.13 Ligand excluded by PLIP PEG.16: 3 residues within 4Å: Chain A: I.335, R.373, Y.375 Ligand excluded by PLIP PEG.17: 4 residues within 4Å: Chain A: F.309, Q.313, L.371, R.373 Ligand excluded by PLIP PEG.18: 6 residues within 4Å: Chain A: R.13, V.136, G.137, E.148, A.149, D.150 Ligand excluded by PLIP PEG.40: 5 residues within 4Å: Chain B: N.218, E.219, N.220, E.221 Ligands: EDO.25 Ligand excluded by PLIP PEG.41: 2 residues within 4Å: Chain B: R.13, R.38 Ligand excluded by PLIP PEG.42: 7 residues within 4Å: Chain B: W.173, C.294, G.344, A.347, A.348 Ligands: BME.21, SO4.23 Ligand excluded by PLIP PEG.43: 3 residues within 4Å: Chain B: R.331, R.373, Y.375 Ligand excluded by PLIP PEG.44: 4 residues within 4Å: Chain B: F.309, Q.313, L.371, R.373 Ligand excluded by PLIP PEG.45: 4 residues within 4Å: Chain B: G.192, H.193 Chain C: G.192, H.193 Ligand excluded by PLIP PEG.46: 6 residues within 4Å: Chain B: N.88, K.89, S.90 Chain D: N.88, K.89, S.90 Ligand excluded by PLIP PEG.47: 6 residues within 4Å: Chain B: R.13, V.136, G.137, E.148, A.149, D.150 Ligand excluded by PLIP PEG.68: 4 residues within 4Å: Chain C: F.205, A.348, N.349, R.350 Ligand excluded by PLIP PEG.69: 6 residues within 4Å: Chain A: N.88, K.89, S.90 Chain C: N.88, K.89, S.90 Ligand excluded by PLIP PEG.70: 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 PEG.71: 3 residues within 4Å: Chain C: R.118, A.119, G.121 Ligand excluded by PLIP PEG.72: 3 residues within 4Å: Chain C: V.131, A.132, S.165 Ligand excluded by PLIP PEG.95: 3 residues within 4Å: Chain D: V.131, A.132, S.165 Ligand excluded by PLIP PEG.96: 7 residues within 4Å: Chain C: H.57, L.69, W.377 Chain D: H.57, R.372, S.376, W.377 Ligand excluded by PLIP PEG.97: 5 residues within 4Å: Chain A: G.192, H.193 Chain D: L.191, G.192, H.193 Ligand excluded by PLIP

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

PGE.19: 5 residues within 4Å: Chain A: R.338, E.364, R.367, Y.375 Chain B: Q.74 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.74, A:R.367, A:R.367 PGE.48: 4 residues within 4Å: Chain B: W.206 Chain D: F.205, A.348, N.349 No protein-ligand interaction detected (PLIP)

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.49: 7 residues within 4Å: Chain A: Q.74 Chain B: R.338, E.364, R.367, Y.375, P.378, Q.379 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.367, B:R.367, B:Q.379, B:Q.379 PG4.73: 6 residues within 4Å: Chain C: I.183, V.184, P.185, N.218, N.220, E.221 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.221 PG4.98: 5 residues within 4Å: Chain D: V.184, P.185, N.218, N.220, E.221 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.218 Water bridges: D:N.220

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
C

D
D

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

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