SMTL ID : 2yob.1

High resolution AGXT_M structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 14 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 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.108, A:W.108, A:V.185, A:V.185, A:A.186 Hydrogen bonds: A:G.82, A:H.83, A:S.158, A:S.158, A:Q.208, A:Q.208, B:Y.260, B:Y.260, B:T.263, B:T.263 Salt bridges: A:H.83, A:K.209 pi-Stacking: A:W.108 PLP.8: 14 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 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.108, B:W.108, B:V.185, B:A.186, B:K.209 Hydrogen bonds: B:G.82, B:H.83, B:S.158, B:S.158, B:Q.208, A:T.263, A:T.263 Salt bridges: B:H.83, B:K.209 pi-Stacking: B:W.108, B:W.108

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.2: 5 residues within 4Å: Chain A: K.245, W.246, N.249, D.254, M.259 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.249, A:D.254 Water bridges: A:N.249, A:N.249, A:M.259 BTB.10: 7 residues within 4Å: Chain B: K.245, W.246, N.249, D.254, Q.256, M.259 Ligands: GOL.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.249, B:N.249, B:D.254 Water bridges: B:D.243, B:W.246

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

SO4.3: 3 residues within 4Å: Chain A: H.4, K.5 Chain B: R.197 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.197 Hydrogen bonds: A:H.4, A:K.5 SO4.9: 1 residues within 4Å: Chain B: R.258 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.258 Salt bridges: B:R.258

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: N.72, D.196, S.223, D.224 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.224 Water bridges: A:N.72, A:D.196, A:S.223, A:S.223, A:K.225 GOL.5: 5 residues within 4Å: Chain A: S.50, K.51 Chain B: Q.23, M.340, E.346 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.51, B:Q.23, B:E.346, B:E.346 GOL.6: 4 residues within 4Å: Chain A: M.38, A.39, G.42 Chain B: G.42 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.42 Water bridges: B:M.38, A:A.39 GOL.7: 3 residues within 4Å: Chain A: V.336, S.337, M.340 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.346, A:I.347, A:I.347 GOL.11: 2 residues within 4Å: Chain B: T.135, L.136 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.136 Water bridges: B:H.133, B:T.135, B:Q.137 GOL.12: 3 residues within 4Å: Chain B: K.236, W.246 Ligands: BTB.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:K.236, B:K.245, A:R.118, A:R.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mesa-Torres, N. et al., The Role of Protein Denaturation Energetics and Molecular Chaperones in the Aggregation and Mistargeting of Mutants Causing Primary Hyperoxaluria Type I. Plos One (2013)

Release Date

2013-10-30

Peptides

SERINE--PYRUVATE AMINOTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SERINE--PYRUVATE AMINOTRANSFERASE