SMTL ID : 2z9x.1

Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxyl-L-alanine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: P.4, E.5, H.6 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: K.218, R.225, V.232 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: P.22, E.23, R.26 Chain C: R.30, T.31 Chain D: D.8 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.26 Chain C: R.30 Ligands: SO4.28 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: P.4, E.5, H.6 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: R.309, P.311, D.312 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain B: P.22, E.23, R.26 Chain C: D.8 Chain D: R.30, T.31 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain B: R.26 Chain D: G.27, R.30, V.258 Ligands: SO4.39 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain C: P.4, E.5, H.6 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: K.218, R.225, V.232 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain A: R.30, T.31 Chain B: D.8 Chain C: P.22, E.23, R.26 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain A: R.30 Chain C: R.26 Ligands: SO4.4 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain D: P.4, E.5, H.6 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain D: R.309, P.311, D.312 Ligand excluded by PLIP SO4.38: 6 residues within 4Å: Chain A: D.8 Chain B: R.30, T.31 Chain D: P.22, E.23, R.26 Ligand excluded by PLIP SO4.39: 5 residues within 4Å: Chain B: G.27, R.30, V.258 Chain D: R.26 Ligands: SO4.15 Ligand excluded by PLIP

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: P.68, G.193, P.194, N.195, K.196 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: P.68, G.193, P.194, N.195, K.196 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain C: P.68, G.193, P.194, N.195, K.196 Ligand excluded by PLIP CL.40: 5 residues within 4Å: Chain D: P.68, G.193, P.194, N.195, K.196 Ligand excluded by PLIP

4 x ALA: ALANINE(Non-covalent)

ALA.6: 9 residues within 4Å: Chain A: G.16, Y.94, T.145, P.146, R.335, R.344 Chain B: T.247 Ligands: PXL.7, GOL.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.16, A:Y.94 Water bridges: A:T.145, A:T.145 Salt bridges: A:R.344 ALA.17: 9 residues within 4Å: Chain A: T.247 Chain B: G.16, Y.94, T.145, P.146, R.335, R.344 Ligands: PXL.18, GOL.21 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.16, B:Y.94, B:Y.94 Water bridges: B:T.145, B:T.145, A:T.247 Salt bridges: B:R.344 ALA.30: 9 residues within 4Å: Chain C: G.16, Y.94, T.145, P.146, R.335, R.344 Chain D: T.247 Ligands: PXL.31, GOL.34 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.16, C:Y.94 Salt bridges: C:R.344 ALA.41: 9 residues within 4Å: Chain C: T.247 Chain D: G.16, Y.94, T.145, P.146, R.335, R.344 Ligands: PXL.42, GOL.45 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.16, D:Y.94 Water bridges: D:K.196 Salt bridges: D:R.344

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

PXL.7: 12 residues within 4Å: Chain A: E.67, P.68, V.69, Y.94, C.141, H.143, T.145, D.170, V.172, S.173, K.196 Ligands: ALA.6 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.94, A:V.172, A.6 Hydrogen bonds: A:E.67, A:T.145, A:T.145, A:K.196 pi-Stacking: A:Y.94 PXL.18: 13 residues within 4Å: Chain B: E.67, P.68, V.69, L.72, Y.94, C.141, H.143, T.145, D.170, V.172, S.173, K.196 Ligands: ALA.17 9 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrophobic interactions: B:Y.94, B:V.172, A.17 Hydrogen bonds: B:E.67, B:T.145, B:T.145, B:K.196 pi-Stacking: B:Y.94 Water bridges: A:T.247 PXL.31: 12 residues within 4Å: Chain C: E.67, P.68, V.69, Y.94, C.141, H.143, T.145, D.170, V.172, S.173, K.196 Ligands: ALA.30 8 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.94, C:V.172, A.30 Hydrogen bonds: C:E.67, C:T.145, C:K.196 pi-Stacking: C:Y.94 Water bridges: D:T.247 PXL.42: 13 residues within 4Å: Chain D: E.67, P.68, V.69, L.72, Y.94, C.141, H.143, T.145, D.170, V.172, S.173, K.196 Ligands: ALA.41 8 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.94, D:V.172, A.41 Hydrogen bonds: D:E.67, D:T.145, D:K.196 pi-Stacking: D:Y.94 Water bridges: C:T.247

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: S.297, D.298, S.299 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: V.93, Y.94, G.97, W.101, R.335 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: S.333, G.334, R.335, R.344 Chain B: Y.34, Y.36 Ligands: ALA.6 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: I.11, T.12, N.19, P.350, T.351, Y.356 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain B: S.297, D.298, S.299 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: V.93, Y.94, G.97, W.101, R.335 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain A: Y.34, Y.36 Chain B: S.333, G.334, R.335, R.344 Ligands: ALA.17 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: I.11, T.12, N.19, P.350, T.351, Y.356 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain A: V.69, W.101 Chain B: A.226, S.227, M.228, D.233, P.245, F.246 Ligand excluded by PLIP GOL.24: 3 residues within 4Å: Chain B: K.218, R.225, V.232 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain C: S.297, D.298, S.299 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain C: V.93, Y.94, G.97, W.101, R.335 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain C: S.333, G.334, R.335, R.344 Chain D: Y.34, Y.36 Ligands: ALA.30 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain C: I.11, T.12, N.19, P.350, T.351, Y.356 Ligand excluded by PLIP GOL.43: 3 residues within 4Å: Chain D: S.297, D.298, S.299 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain D: V.93, Y.94, G.97, W.101, R.335 Ligand excluded by PLIP GOL.45: 7 residues within 4Å: Chain C: Y.34, Y.36 Chain D: S.333, G.334, R.335, R.344 Ligands: ALA.41 Ligand excluded by PLIP GOL.46: 6 residues within 4Å: Chain D: I.11, T.12, N.19, P.350, T.351, Y.356 Ligand excluded by PLIP GOL.47: 8 residues within 4Å: Chain C: V.69, W.101 Chain D: A.226, S.227, M.228, D.233, P.245, F.246 Ligand excluded by PLIP GOL.48: 3 residues within 4Å: Chain D: K.218, R.225, V.232 Ligand excluded by PLIP

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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