SMTL ID : 1h0c.1

The crystal structure of human alanine:glyoxylate aminotransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: S.81, G.82, H.83, W.108, G.156, S.158, D.183, V.185, A.186, Q.208, K.209 Chain B: Y.260, H.262, T.263 Ligands: AOA.2 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.185, A:V.185, A:K.209 Hydrogen bonds: A:G.82, A:H.83, A:S.158, A:Q.208, B:Y.260, B:T.263 Water bridges: A:Q.208 Salt bridges: A:H.83, A:K.209 pi-Stacking: A:W.108, A:W.108 PLP.9: 15 residues within 4Å: Chain A: Y.260, H.262, T.263 Chain B: S.81, G.82, H.83, W.108, G.156, S.158, D.183, V.185, A.186, Q.208, K.209 Ligands: AOA.10 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.185, B:V.185, B:K.209 Hydrogen bonds: B:G.82, B:H.83, B:S.158, B:Q.208, A:Y.260, A:Y.260, A:T.263, A:T.263 Water bridges: B:Q.208, B:K.209 Salt bridges: B:H.83, B:K.209 pi-Stacking: B:W.108, B:W.108

2 x AOA: (AMINOOXY)ACETIC ACID(Non-covalent)

AOA.2: 8 residues within 4Å: Chain A: P.28, G.29, S.158, K.209, L.351, R.360 Chain B: Y.260 Ligands: PLP.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.29, A:S.158 Salt bridges: A:R.360 Water bridges: B:T.263 AOA.10: 8 residues within 4Å: Chain A: Y.260 Chain B: P.28, G.29, S.158, K.209, L.351, R.360 Ligands: PLP.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.29, B:S.158, B:K.209 Salt bridges: B:R.360

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.333, V.336, S.337 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.333 GOL.4: 2 residues within 4Å: Chain A: L.24, F.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.343 Water bridges: A:R.375 GOL.5: 7 residues within 4Å: Chain A: Q.290, E.293, A.294, A.368, T.369, R.370, E.371 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.293, A:E.293, A:A.294, A:R.370, A:E.371 GOL.6: 7 residues within 4Å: Chain A: P.17, L.18, S.19 Chain B: D.52, Q.55, I.56, R.273 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.52, B:D.52, B:R.273, A:P.17, A:S.19 Water bridges: B:D.52, A:S.19 GOL.7: 4 residues within 4Å: Chain A: I.107, Q.110, R.111, D.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.111, A:D.114 GOL.8: 2 residues within 4Å: Chain A: L.278, C.366 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.212, A:Q.282, A:G.365, A:C.366 GOL.11: 3 residues within 4Å: Chain B: R.333, V.336, S.337 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.333 GOL.12: 2 residues within 4Å: Chain B: L.24, F.343 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.343 Water bridges: B:R.375 GOL.13: 7 residues within 4Å: Chain B: Q.290, E.293, A.294, A.368, T.369, R.370, E.371 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.293, B:A.294, B:R.370, B:E.371 GOL.14: 7 residues within 4Å: Chain A: D.52, Q.55, I.56, R.273 Chain B: P.17, L.18, S.19 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.52, A:R.273, B:P.17, B:S.19 Water bridges: A:D.52, B:S.19 GOL.15: 4 residues within 4Å: Chain B: I.107, Q.110, R.111, D.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.111, B:D.114, B:D.114 GOL.16: 2 residues within 4Å: Chain B: L.278, C.366 4 PLIP interactions: 4 interactions with chain B Water bridges: B:N.212, B:Q.282, B:G.365, B:C.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Crystal Structure of Alanine:Glyoxylate Aminotransferase and the Relationship between Genotype and Enzymatic Phenotype in Primary Hyperoxaluria Type 1. J.Mol.Biol. (2003)

Release Date

2003-06-12

Peptides

SERINE--GLYOXYLATE AMINOTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

SERINE--GLYOXYLATE AMINOTRANSFERASE

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