SMTL ID : 4b98.1

The structure of the omega aminotransferase from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

4 x PXG: 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID(Non-covalent)

PXG.1: 19 residues within 4Å: Chain A: L.60, W.61, S.119, G.120, S.121, Y.153, H.154, G.155, E.226, S.231, D.259, V.261, I.262, K.288, R.414, Q.421 Chain B: F.89, Y.326, T.327 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.60, A:L.60, A:E.226, A:V.261, B:F.89 Hydrogen bonds: A:W.61, A:G.120, A:S.121, A:K.288, A:Q.421, B:T.327, B:T.327, B:T.327 Water bridges: A:E.226, A:R.414, B:T.327, B:Y.328 Salt bridges: A:R.414 pi-Stacking: A:Y.153 PXG.5: 19 residues within 4Å: Chain A: F.89, Y.326, T.327 Chain B: W.61, S.119, G.120, S.121, Y.153, H.154, G.155, E.226, G.230, S.231, D.259, V.261, I.262, K.288, R.414, Q.421 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:F.89, B:Y.153, B:E.226, B:V.261 Hydrogen bonds: A:T.327, A:T.327, B:G.120, B:S.121, B:S.121, B:K.288, B:K.288, B:Q.421 Water bridges: A:Y.328, B:R.414 Salt bridges: B:R.414 pi-Stacking: B:Y.153 PXG.9: 20 residues within 4Å: Chain C: L.60, W.61, S.119, G.120, S.121, Y.153, H.154, G.155, E.226, G.230, S.231, D.259, V.261, I.262, K.288, R.414, Q.421 Chain D: F.89, Y.326, T.327 18 PLIP interactions: 4 interactions with chain D, 14 interactions with chain C Hydrophobic interactions: D:F.89, C:L.60, C:Y.153, C:E.226, C:V.261, C:V.261 Hydrogen bonds: D:T.327, D:T.327, C:G.120, C:S.121, C:S.121, C:K.288, C:K.288, C:Q.421 Water bridges: D:Y.328, C:S.121 Salt bridges: C:R.414 pi-Stacking: C:Y.153 PXG.12: 18 residues within 4Å: Chain C: F.89, Y.326, T.327 Chain D: W.61, S.119, G.120, S.121, Y.153, H.154, G.155, E.226, S.231, D.259, V.261, I.262, K.288, R.414, Q.421 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.153, D:E.226, D:V.261, D:V.261, C:F.89 Hydrogen bonds: D:W.61, D:G.120, D:S.121, D:S.121, D:K.288, D:K.288, D:Q.421, C:T.327 Salt bridges: D:R.414 pi-Stacking: D:Y.153 Water bridges: C:T.327, C:Y.328

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.2: 8 residues within 4Å: Chain A: M.196, V.239, G.240, Y.241, L.242, Q.243, F.277, G.278 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.240, A:G.240, A:L.242, A:Q.243, A:F.277 Water bridges: A:Y.241, A:Y.241 PLP.6: 8 residues within 4Å: Chain B: M.196, V.239, G.240, Y.241, L.242, Q.243, F.277, G.278 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.240, B:G.240, B:L.242, B:Q.243, B:F.277 Water bridges: B:Y.241, B:Y.241, B:Q.243 PLP.10: 8 residues within 4Å: Chain C: M.196, V.239, G.240, Y.241, L.242, Q.243, F.277, G.278 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.240, C:L.242, C:Q.243 Water bridges: C:Y.241, C:Y.241 PLP.13: 8 residues within 4Å: Chain D: M.196, V.239, G.240, Y.241, L.242, Q.243, F.277, G.278 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.240, D:L.242, D:Q.243 Water bridges: D:Y.241, D:Y.241, D:Q.243

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: D.180 Chain D: D.180 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: D:D.180, A:D.180, H2O.9, H2O.9, H2O.9, H2O.16 CA.7: 2 residues within 4Å: Chain B: D.180 Chain C: D.180 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: B:D.180, C:D.180, H2O.23, H2O.23, H2O.23, H2O.30

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

CL.4: 4 residues within 4Å: Chain A: F.322, S.323 Chain B: M.172, F.173 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: M.172, F.173 Chain B: F.322, S.323 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain C: F.322, S.323 Chain D: M.172, F.173 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: M.172, F.173 Chain D: F.322, S.323 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sayer, C. et al., Structural Studies with Pseudomonas and Chromobacterium [Omega]-Aminotransferases Provide Insights Into Their Differing Substrate Specificity. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-03-27

Peptides

BETA-ALANINE--PYRUVATE TRANSAMINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BETA-ALANINE--PYRUVATE TRANSAMINASE

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