SMTL ID : 3lsm.1

Pyranose 2-oxidase H167A mutant with flavin N(5) sulfite adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x SFD: (S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHOXY)(HYDROXY)PHOSPHORYLOXY)(HYDROXY)PHOSPHORYLOXY)-2,3,4-TRIHYDROXYPENTYL)-7,8-DIMETHYL-2,4-DIOXO-2,3,4,4A-TETRAHYDROBENZO[G]PTERIDINE-5(10H)-SULFONIC ACID(Non-covalent)

SFD.1: 35 residues within 4Å: Chain A: V.52, G.53, G.55, P.56, I.57, F.75, D.76, I.77, I.107, T.158, R.159, V.160, G.163, M.164, S.165, A.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, G.321, H.324, R.472, V.546, L.547, H.548, G.582, C.583, N.593, P.594, T.595 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.107, A:L.547 Hydrogen bonds: A:G.55, A:I.57, A:G.58, A:I.77, A:G.78, A:V.160, A:G.163, A:M.164, A:S.165, A:T.169, A:T.169, A:A.171, A:A.171, A:C.283, A:C.283, A:N.593, A:T.595, A:T.595 Water bridges: A:G.321, A:Y.456, A:R.472, A:L.547, A:L.596 Salt bridges: A:R.472, A:H.548 SFD.6: 34 residues within 4Å: Chain B: V.52, G.53, G.55, P.56, I.57, D.76, I.77, I.107, T.158, R.159, V.160, G.163, M.164, S.165, A.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, G.321, H.324, R.472, V.546, L.547, H.548, G.582, C.583, N.593, P.594, T.595 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:I.107, B:T.169, B:L.547 Hydrogen bonds: B:G.55, B:I.57, B:G.58, B:I.77, B:G.78, B:V.160, B:G.163, B:M.164, B:S.165, B:T.169, B:T.169, B:A.171, B:A.171, B:C.283, B:C.283, B:N.593, B:T.595 Water bridges: B:G.321, B:Y.456, B:R.472, B:L.596 Salt bridges: B:R.472, B:H.548 SFD.10: 35 residues within 4Å: Chain C: V.52, G.53, G.55, P.56, I.57, F.75, D.76, I.77, I.107, T.158, R.159, V.160, G.163, M.164, S.165, A.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, G.321, H.324, R.472, V.546, L.547, H.548, G.582, C.583, N.593, P.594, T.595 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:I.107, C:L.547 Hydrogen bonds: C:G.55, C:I.57, C:G.58, C:I.77, C:G.78, C:V.160, C:G.163, C:M.164, C:S.165, C:T.169, C:T.169, C:A.171, C:A.171, C:C.283, C:C.283, C:N.593, C:T.595, C:T.595 Water bridges: C:G.321, C:R.472, C:R.472, C:L.547, C:L.596 Salt bridges: C:R.472, C:H.548 SFD.15: 34 residues within 4Å: Chain D: V.52, G.53, G.55, P.56, I.57, D.76, I.77, I.107, T.158, R.159, V.160, G.163, M.164, S.165, A.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, G.321, H.324, R.472, V.546, L.547, H.548, G.582, C.583, N.593, P.594, T.595 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:I.107, D:T.169, D:L.547 Hydrogen bonds: D:G.55, D:I.57, D:G.58, D:I.77, D:G.78, D:V.160, D:G.163, D:M.164, D:S.165, D:T.169, D:T.169, D:A.171, D:A.171, D:C.283, D:C.283, D:N.593, D:T.595, D:T.595 Water bridges: D:G.321, D:R.472, D:L.596 Salt bridges: D:R.472, D:H.548

8 x SO3: SULFITE ION(Non-covalent)

SO3.2: 4 residues within 4Å: Chain A: R.571, F.573, G.574, F.575 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.571, A:R.571, A:G.574 Water bridges: A:N.567 SO3.3: 3 residues within 4Å: Chain A: S.293, G.574, K.576 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.293, A:G.574 SO3.7: 5 residues within 4Å: Chain B: R.571, F.573, G.574, F.575, K.576 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.571, B:R.571, B:G.574, B:K.576, B:K.576 Water bridges: B:N.567, B:N.567 SO3.8: 6 residues within 4Å: Chain B: H.415, Q.418, H.419, P.427, F.428, E.429 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.415, B:F.428, B:E.429, B:E.429 Water bridges: B:H.415 Salt bridges: B:E.429 SO3.11: 4 residues within 4Å: Chain C: R.571, F.573, G.574, F.575 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.571, C:R.571, C:G.574 Water bridges: C:N.567 SO3.12: 3 residues within 4Å: Chain C: S.293, G.574, K.576 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.293, C:G.574 SO3.16: 5 residues within 4Å: Chain D: R.571, F.573, G.574, F.575, K.576 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.571, D:R.571, D:G.574, D:K.576, D:K.576 Water bridges: D:N.567, D:N.567 SO3.17: 6 residues within 4Å: Chain D: H.415, Q.418, H.419, P.427, F.428, E.429 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.415, D:F.428, D:E.429 Water bridges: D:H.415 Salt bridges: D:E.429

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.4: 7 residues within 4Å: Chain A: R.63, E.64, G.67, A.68, K.201, Y.205, K.610 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.63, A:R.63, A:K.201, A:K.201, A:Y.205, A:K.610 GLC.13: 7 residues within 4Å: Chain C: R.63, E.64, G.67, A.68, K.201, Y.205, K.610 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.63, C:R.63, C:K.201, C:K.201, C:K.610

4 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.5: 8 residues within 4Å: Chain A: P.144, E.145, Q.146, D.147, P.148, R.339 Chain C: S.134, F.136 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.145 12P.9: 8 residues within 4Å: Chain B: P.144, E.145, Q.146, D.147, P.148, R.339 Chain D: S.134, F.136 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.339 12P.14: 8 residues within 4Å: Chain A: S.134, F.136 Chain C: P.144, E.145, Q.146, D.147, P.148, R.339 No protein-ligand interaction detected (PLIP) 12P.18: 8 residues within 4Å: Chain B: S.134, F.136 Chain D: P.144, E.145, Q.146, D.147, P.148, R.339 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, T.C. et al., H-bonding and positive charge at the N5/O4 locus are critical for covalent flavin attachment in trametes pyranose 2-oxidase. J.Mol.Biol. (2010)

Release Date

2010-08-25

Peptides

Pyranose 2-oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyranose 2-oxidase

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