SMTL ID : 1al7.2 (1 other biounit)

THREE-DIMENSIONAL STRUCTURES OF GLYCOLATE OXIDASE WITH BOUND ACTIVE-SITE INHIBITORS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-octamer

Ligands

8 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: Y.24, Y.25, A.76, P.77, T.78, A.79, S.106, Q.127, Y.129, T.155, K.230, S.252, H.254, G.255, R.257, D.285, G.286, G.287, R.289, I.307, G.308, R.309 Ligands: HST.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.24, A:Y.25, A:T.78, A:R.309 Hydrogen bonds: A:P.77, A:S.106, A:Q.127, A:Y.129, A:T.155, A:K.230, A:K.230, A:S.252, A:G.286, A:G.287, A:G.308, A:R.309 Water bridges: A:W.108, A:G.255, A:R.289, A:R.289, A:R.309, A:R.309 Salt bridges: A:R.289, A:R.309 FMN.3: 23 residues within 4Å: Chain B: Y.24, Y.25, A.76, P.77, T.78, A.79, S.106, Q.127, Y.129, T.155, K.230, S.252, H.254, G.255, R.257, D.285, G.286, G.287, R.289, I.307, G.308, R.309 Ligands: HST.4 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:Y.24, B:Y.25, B:T.78, B:R.309 Hydrogen bonds: B:P.77, B:S.106, B:Q.127, B:Y.129, B:T.155, B:K.230, B:K.230, B:S.252, B:G.286, B:G.287, B:G.308, B:R.309 Water bridges: B:W.108, B:G.255, B:R.289, B:R.289, B:R.309, B:R.309 Salt bridges: B:R.289, B:R.309 FMN.5: 23 residues within 4Å: Chain C: Y.24, Y.25, A.76, P.77, T.78, A.79, S.106, Q.127, Y.129, T.155, K.230, S.252, H.254, G.255, R.257, D.285, G.286, G.287, R.289, I.307, G.308, R.309 Ligands: HST.6 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:Y.24, C:Y.25, C:T.78, C:R.309 Hydrogen bonds: C:P.77, C:S.106, C:Q.127, C:Y.129, C:T.155, C:K.230, C:K.230, C:S.252, C:G.286, C:G.287, C:G.308, C:R.309 Water bridges: C:W.108, C:G.255, C:R.289, C:R.289, C:R.309, C:R.309 Salt bridges: C:R.289, C:R.309 FMN.7: 23 residues within 4Å: Chain D: Y.24, Y.25, A.76, P.77, T.78, A.79, S.106, Q.127, Y.129, T.155, K.230, S.252, H.254, G.255, R.257, D.285, G.286, G.287, R.289, I.307, G.308, R.309 Ligands: HST.8 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:Y.24, D:Y.25, D:T.78, D:R.309 Hydrogen bonds: D:P.77, D:S.106, D:Q.127, D:Y.129, D:T.155, D:K.230, D:K.230, D:S.252, D:G.286, D:G.287, D:G.308, D:R.309 Water bridges: D:W.108, D:G.255, D:R.289, D:R.289, D:R.309, D:R.309 Salt bridges: D:R.289, D:R.309 FMN.9: 23 residues within 4Å: Chain E: Y.24, Y.25, A.76, P.77, T.78, A.79, S.106, Q.127, Y.129, T.155, K.230, S.252, H.254, G.255, R.257, D.285, G.286, G.287, R.289, I.307, G.308, R.309 Ligands: HST.10 22 PLIP interactions: 22 interactions with chain E Hydrophobic interactions: E:Y.24, E:Y.25, E:T.78, E:R.309 Hydrogen bonds: E:P.77, E:S.106, E:Q.127, E:K.230, E:K.230, E:S.252, E:G.286, E:G.287, E:G.308, E:R.309 Water bridges: E:W.108, E:G.255, E:R.289, E:R.289, E:R.309, E:R.309 Salt bridges: E:R.289, E:R.309 FMN.11: 23 residues within 4Å: Chain F: Y.24, Y.25, A.76, P.77, T.78, A.79, S.106, Q.127, Y.129, T.155, K.230, S.252, H.254, G.255, R.257, D.285, G.286, G.287, R.289, I.307, G.308, R.309 Ligands: HST.12 22 PLIP interactions: 22 interactions with chain F Hydrophobic interactions: F:Y.24, F:Y.25, F:T.78, F:R.309 Hydrogen bonds: F:P.77, F:S.106, F:Q.127, F:K.230, F:K.230, F:S.252, F:G.286, F:G.287, F:G.308, F:R.309 Water bridges: F:W.108, F:G.255, F:R.289, F:R.289, F:R.309, F:R.309 Salt bridges: F:R.289, F:R.309 FMN.13: 23 residues within 4Å: Chain G: Y.24, Y.25, A.76, P.77, T.78, A.79, S.106, Q.127, Y.129, T.155, K.230, S.252, H.254, G.255, R.257, D.285, G.286, G.287, R.289, I.307, G.308, R.309 Ligands: HST.14 22 PLIP interactions: 22 interactions with chain G Hydrophobic interactions: G:Y.24, G:Y.25, G:T.78, G:R.309 Hydrogen bonds: G:P.77, G:S.106, G:Q.127, G:K.230, G:K.230, G:S.252, G:G.286, G:G.287, G:G.308, G:R.309 Water bridges: G:W.108, G:G.255, G:R.289, G:R.289, G:R.309, G:R.309 Salt bridges: G:R.289, G:R.309 FMN.15: 23 residues within 4Å: Chain H: Y.24, Y.25, A.76, P.77, T.78, A.79, S.106, Q.127, Y.129, T.155, K.230, S.252, H.254, G.255, R.257, D.285, G.286, G.287, R.289, I.307, G.308, R.309 Ligands: HST.16 22 PLIP interactions: 22 interactions with chain H Hydrophobic interactions: H:Y.24, H:Y.25, H:T.78, H:R.309 Hydrogen bonds: H:P.77, H:S.106, H:Q.127, H:K.230, H:K.230, H:S.252, H:G.286, H:G.287, H:G.308, H:R.309 Water bridges: H:W.108, H:G.255, H:R.289, H:R.289, H:R.309, H:R.309 Salt bridges: H:R.289, H:R.309

8 x HST: 4-CARBOXY-5-(1-PENTYL)HEXYLSULFANYL-1,2,3-TRIAZOLE(Non-covalent)

HST.2: 12 residues within 4Å: Chain A: Y.24, A.79, W.108, Y.129, Y.131, L.161, R.164, F.172, I.207, H.254, R.257 Ligands: FMN.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.108, A:Y.129, A:Y.129, A:Y.131, A:L.161, A:L.161, A:F.172, A:F.172, A:I.207, A:I.207 Hydrogen bonds: A:Y.24, A:Y.129 Water bridges: A:S.106, A:T.158 Salt bridges: A:R.164, A:H.254, A:R.257 HST.4: 12 residues within 4Å: Chain B: Y.24, A.79, W.108, Y.129, Y.131, L.161, R.164, F.172, I.207, H.254, R.257 Ligands: FMN.3 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.108, B:Y.129, B:Y.129, B:Y.131, B:L.161, B:L.161, B:F.172, B:F.172, B:I.207, B:I.207 Hydrogen bonds: B:Y.24, B:Y.129 Water bridges: B:S.106, B:T.158 Salt bridges: B:R.164, B:H.254, B:R.257 HST.6: 12 residues within 4Å: Chain C: Y.24, A.79, W.108, Y.129, Y.131, L.161, R.164, F.172, I.207, H.254, R.257 Ligands: FMN.5 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:W.108, C:Y.129, C:Y.129, C:Y.131, C:L.161, C:L.161, C:F.172, C:F.172, C:I.207, C:I.207 Hydrogen bonds: C:Y.24, C:Y.129 Water bridges: C:S.106, C:T.158 Salt bridges: C:R.164, C:H.254, C:R.257 HST.8: 12 residues within 4Å: Chain D: Y.24, A.79, W.108, Y.129, Y.131, L.161, R.164, F.172, I.207, H.254, R.257 Ligands: FMN.7 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:W.108, D:Y.129, D:Y.129, D:Y.131, D:L.161, D:L.161, D:F.172, D:F.172, D:I.207, D:I.207 Hydrogen bonds: D:Y.24, D:Y.129 Water bridges: D:S.106, D:T.158 Salt bridges: D:R.164, D:H.254, D:R.257 HST.10: 12 residues within 4Å: Chain E: Y.24, A.79, W.108, Y.129, Y.131, L.161, R.164, F.172, I.207, H.254, R.257 Ligands: FMN.9 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:W.108, E:Y.129, E:Y.129, E:Y.131, E:L.161, E:L.161, E:F.172, E:F.172, E:I.207, E:I.207 Hydrogen bonds: E:Y.24, E:Y.24 Water bridges: E:S.106, E:R.164 Salt bridges: E:R.164, E:H.254, E:R.257 HST.12: 12 residues within 4Å: Chain F: Y.24, A.79, W.108, Y.129, Y.131, L.161, R.164, F.172, I.207, H.254, R.257 Ligands: FMN.11 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:W.108, F:Y.129, F:Y.129, F:Y.131, F:L.161, F:L.161, F:F.172, F:F.172, F:I.207, F:I.207 Hydrogen bonds: F:Y.24, F:Y.24 Water bridges: F:S.106, F:R.164 Salt bridges: F:R.164, F:H.254, F:R.257 HST.14: 12 residues within 4Å: Chain G: Y.24, A.79, W.108, Y.129, Y.131, L.161, R.164, F.172, I.207, H.254, R.257 Ligands: FMN.13 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:W.108, G:Y.129, G:Y.129, G:Y.131, G:L.161, G:L.161, G:F.172, G:F.172, G:I.207, G:I.207 Hydrogen bonds: G:Y.24, G:Y.24 Water bridges: G:S.106, G:R.164 Salt bridges: G:R.164, G:H.254, G:R.257 HST.16: 12 residues within 4Å: Chain H: Y.24, A.79, W.108, Y.129, Y.131, L.161, R.164, F.172, I.207, H.254, R.257 Ligands: FMN.15 17 PLIP interactions: 17 interactions with chain H Hydrophobic interactions: H:W.108, H:Y.129, H:Y.129, H:Y.131, H:L.161, H:L.161, H:F.172, H:F.172, H:I.207, H:I.207 Hydrogen bonds: H:Y.24, H:Y.24 Water bridges: H:S.106, H:R.164 Salt bridges: H:R.164, H:H.254, H:R.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stenberg, K. et al., Three-dimensional structures of glycolate oxidase with bound active-site inhibitors. Protein Sci. (1997)

Release Date

1997-11-12

Peptides

GLYCOLATE OXIDASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

GLYCOLATE OXIDASE

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