SMTL ID : 2z9w.1

Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: G.16, Y.94, P.146, R.335, R.344 Ligands: GOL.15 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.94, A:Y.94 Water bridges: A:T.145, A:R.344, A:R.344, B:T.247 Salt bridges: A:R.335, A:R.344 SO4.2: 3 residues within 4Å: Chain A: K.218, R.225, V.232 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.235 Salt bridges: A:K.218, A:R.225 SO4.3: 6 residues within 4Å: Chain A: P.22, E.23, R.26 Chain C: R.30, T.31 Chain D: D.8 6 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: D:D.8, C:T.31, C:T.31, C:T.31 Water bridges: A:R.26 Salt bridges: A:R.26 SO4.8: 6 residues within 4Å: Chain B: G.16, Y.94, P.146, R.335, R.344 Ligands: GOL.7 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.94 Water bridges: B:G.16, B:R.335, B:R.335, B:R.344, B:R.344, B:R.344, B:R.344, A:T.247 Salt bridges: B:K.196, B:R.335, B:R.344 SO4.9: 3 residues within 4Å: Chain B: P.4, E.5, H.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.5, B:H.6 Salt bridges: B:H.6 SO4.10: 4 residues within 4Å: Chain B: R.309, P.311, D.312, R.373 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.312 Water bridges: B:R.309, B:R.309, B:R.373, B:R.373 Salt bridges: B:R.309 SO4.11: 6 residues within 4Å: Chain B: P.22, E.23, R.26 Chain C: D.8 Chain D: R.30, T.31 7 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: B:E.23, C:D.8, D:T.31, D:T.31, D:T.31 Water bridges: B:R.26 Salt bridges: B:R.26 SO4.17: 6 residues within 4Å: Chain C: G.16, Y.94, P.146, R.335, R.344 Ligands: GOL.31 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.94 Water bridges: C:R.344, C:R.344, C:R.344 Salt bridges: C:R.335, C:R.344 SO4.18: 3 residues within 4Å: Chain C: K.218, R.225, V.232 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.218, C:R.225 SO4.19: 6 residues within 4Å: Chain A: R.30, T.31 Chain B: D.8 Chain C: P.22, E.23, R.26 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:E.23, A:T.31, A:T.31 Water bridges: C:R.26 Salt bridges: C:R.26 SO4.24: 6 residues within 4Å: Chain D: G.16, Y.94, P.146, R.335, R.344 Ligands: GOL.23 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Water bridges: D:G.16, D:R.335, D:R.344, D:R.344, D:R.344, D:R.344, D:R.344, C:T.247 Salt bridges: D:K.196, D:R.335, D:R.344 SO4.25: 3 residues within 4Å: Chain D: P.4, E.5, H.6 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.5, D:H.6 Salt bridges: D:H.6 SO4.26: 4 residues within 4Å: Chain D: R.309, P.311, D.312, R.373 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.312 Water bridges: D:R.309, D:R.309, D:R.373, D:R.373 Salt bridges: D:R.309 SO4.27: 6 residues within 4Å: Chain A: D.8 Chain B: R.30, T.31 Chain D: P.22, E.23, R.26 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:E.23, B:T.31, B:T.31 Water bridges: D:R.26 Salt bridges: D:R.26

4 x PXL: 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE(Covalent)

PXL.4: 12 residues within 4Å: Chain A: E.67, P.68, L.72, Y.94, C.141, H.143, T.145, D.170, V.172, S.173, N.195, K.196 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.94, A:V.172, A:K.196 Hydrogen bonds: A:E.67, A:T.145, A:T.145, A:S.173, A:N.195 pi-Stacking: A:Y.94 PXL.12: 12 residues within 4Å: Chain B: E.67, P.68, L.72, Y.94, C.141, H.143, T.145, D.170, V.172, S.173, N.195, K.196 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.94, B:V.172, B:K.196 Hydrogen bonds: B:E.67, B:T.145, B:T.145 pi-Stacking: B:Y.94 PXL.20: 12 residues within 4Å: Chain C: E.67, P.68, L.72, Y.94, C.141, H.143, T.145, D.170, V.172, S.173, N.195, K.196 9 PLIP interactions: 1 interactions with chain D, 8 interactions with chain C Water bridges: D:T.247 Hydrophobic interactions: C:Y.94, C:V.172, C:K.196 Hydrogen bonds: C:E.67, C:T.145, C:S.173, C:N.195 pi-Stacking: C:Y.94 PXL.28: 12 residues within 4Å: Chain D: E.67, P.68, L.72, Y.94, C.141, H.143, T.145, D.170, V.172, S.173, N.195, K.196 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.94, D:V.172, D:K.196 Hydrogen bonds: D:E.67, D:T.145 pi-Stacking: D:Y.94

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: S.297, D.298, S.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.298, A:S.299, A:S.299 Water bridges: A:S.297 GOL.6: 5 residues within 4Å: Chain A: G.97, F.98, Y.100, W.101 Chain B: A.226 No protein-ligand interaction detected (PLIP) GOL.7: 7 residues within 4Å: Chain A: D.35, Y.36, F.244, F.246, T.247 Chain B: R.335 Ligands: SO4.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.335, A:D.35 Water bridges: A:F.244 GOL.13: 3 residues within 4Å: Chain B: S.297, D.298, S.299 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.298, B:S.299, B:S.299 GOL.14: 3 residues within 4Å: Chain B: G.97, Y.100, W.101 No protein-ligand interaction detected (PLIP) GOL.15: 7 residues within 4Å: Chain A: R.335 Chain B: D.35, Y.36, F.244, F.246, T.247 Ligands: SO4.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.35, A:R.335 Water bridges: B:F.244, B:P.245 GOL.16: 6 residues within 4Å: Chain B: I.11, T.12, N.19, P.350, T.351, Y.356 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.12, B:T.12, B:Y.356 Water bridges: B:T.12 GOL.21: 3 residues within 4Å: Chain C: S.297, D.298, S.299 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.298, C:S.299, C:S.299 Water bridges: C:S.297 GOL.22: 5 residues within 4Å: Chain C: G.97, F.98, Y.100, W.101 Chain D: A.226 No protein-ligand interaction detected (PLIP) GOL.23: 7 residues within 4Å: Chain C: D.35, Y.36, F.244, F.246, T.247 Chain D: R.335 Ligands: SO4.24 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.35, C:Y.36, D:R.335 Water bridges: C:F.244 GOL.29: 3 residues within 4Å: Chain D: S.297, D.298, S.299 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.298, D:S.299, D:S.299 GOL.30: 3 residues within 4Å: Chain D: G.97, Y.100, W.101 No protein-ligand interaction detected (PLIP) GOL.31: 7 residues within 4Å: Chain C: R.335 Chain D: D.35, Y.36, F.244, F.246, T.247 Ligands: SO4.17 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:R.335, D:D.35, D:Y.36 Water bridges: D:F.244, D:P.245 GOL.32: 6 residues within 4Å: Chain D: I.11, T.12, N.19, P.350, T.351, Y.356 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:T.12, D:T.12 Water bridges: D:N.19, A:Y.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshikane, Y. et al., Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099. J.Biol.Chem. (2008)

Release Date

2007-11-06

Peptides

Aspartate aminotransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Aspartate aminotransferase

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