SMTL ID : 2rdt.1

Crystal Structure of Human Glycolate Oxidase (GO) in Complex with CDST

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: Y.43, Y.44, A.96, T.97, A.98, S.125, W.127, Q.147, Y.149, T.175, K.253, S.275, H.277, G.278, R.280, D.308, G.309, G.310, R.312, V.330, G.331, R.332 Ligands: 2RD.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.43, A:Y.44, A:T.97, A:R.332 Hydrogen bonds: A:A.96, A:A.98, A:Q.147, A:Y.149, A:T.175, A:K.253, A:K.253, A:S.275, A:G.278, A:G.309, A:G.310, A:G.331, A:R.332 Water bridges: A:A.96, A:H.277, A:H.277, A:V.311, A:R.332, A:R.332 Salt bridges: A:R.312, A:R.332 FMN.3: 23 residues within 4Å: Chain B: Y.43, Y.44, A.96, T.97, A.98, S.125, W.127, Q.147, Y.149, T.175, K.253, S.275, H.277, G.278, R.280, D.308, G.309, G.310, R.312, V.330, G.331, R.332 Ligands: 2RD.4 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.43, B:Y.44, B:T.97, B:R.332 Hydrogen bonds: B:A.96, B:A.98, B:Q.147, B:Y.149, B:T.175, B:K.253, B:K.253, B:S.275, B:G.278, B:G.309, B:G.310, B:G.331, B:R.332 Water bridges: B:A.96, B:H.277, B:H.277, B:V.311, B:R.332, B:R.332 Salt bridges: B:R.312, B:R.332 FMN.5: 23 residues within 4Å: Chain C: Y.43, Y.44, A.96, T.97, A.98, S.125, W.127, Q.147, Y.149, T.175, K.253, S.275, H.277, G.278, R.280, D.308, G.309, G.310, R.312, V.330, G.331, R.332 Ligands: 2RD.6 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:Y.43, C:Y.44, C:T.97, C:R.332 Hydrogen bonds: C:A.96, C:A.98, C:Q.147, C:Y.149, C:T.175, C:K.253, C:K.253, C:S.275, C:G.278, C:G.309, C:G.310, C:G.331, C:R.332 Water bridges: C:A.96, C:H.277, C:H.277, C:V.311, C:R.332, C:R.332 Salt bridges: C:R.312, C:R.332 FMN.7: 23 residues within 4Å: Chain D: Y.43, Y.44, A.96, T.97, A.98, S.125, W.127, Q.147, Y.149, T.175, K.253, S.275, H.277, G.278, R.280, D.308, G.309, G.310, R.312, V.330, G.331, R.332 Ligands: 2RD.8 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:Y.43, D:Y.44, D:T.97, D:R.332 Hydrogen bonds: D:A.96, D:A.98, D:Q.147, D:Y.149, D:T.175, D:K.253, D:K.253, D:S.275, D:G.278, D:G.309, D:G.310, D:G.331, D:R.332 Water bridges: D:A.96, D:H.277, D:H.277, D:V.311, D:R.332, D:R.332 Salt bridges: D:R.312, D:R.332

4 x 2RD: 5-(dodecylthio)-1H-1,2,3-triazole-4-carboxylic acid(Non-covalent)

2RD.2: 11 residues within 4Å: Chain A: Y.43, M.99, W.127, A.128, T.129, Y.149, R.184, L.222, H.277, R.280 Ligands: FMN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.127, A:W.127, A:T.129, A:L.222 Hydrogen bonds: A:W.127, A:Y.149 Salt bridges: A:R.184, A:H.277, A:R.280 2RD.4: 11 residues within 4Å: Chain B: Y.43, M.99, W.127, A.128, T.129, Y.149, R.184, L.222, H.277, R.280 Ligands: FMN.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.127, B:W.127, B:T.129, B:L.222 Hydrogen bonds: B:W.127, B:Y.149 Salt bridges: B:R.184, B:H.277, B:R.280 2RD.6: 11 residues within 4Å: Chain C: Y.43, M.99, W.127, A.128, T.129, Y.149, R.184, L.222, H.277, R.280 Ligands: FMN.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.127, C:W.127, C:T.129, C:L.222 Hydrogen bonds: C:W.127, C:Y.149 Salt bridges: C:R.184, C:H.277, C:R.280 2RD.8: 11 residues within 4Å: Chain D: Y.43, M.99, W.127, A.128, T.129, Y.149, R.184, L.222, H.277, R.280 Ligands: FMN.7 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.127, D:W.127, D:T.129, D:L.222 Hydrogen bonds: D:W.127, D:Y.149 Salt bridges: D:R.184, D:H.277, D:R.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murray, M.S. et al., Active Site and Loop 4 Movements within Human Glycolate Oxidase: Implications for Substrate Specificity and Drug Design. Biochemistry (2008)

Release Date

2008-02-26

Peptides

Hydroxyacid oxidase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Hydroxyacid oxidase 1

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