SMTL ID : 4jew.1

N-acetylornithine aminotransferase from S. typhimurium complexed with L-canaline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

2 x P00: (2S)-2-azanyl-4-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxy-butanoic acid(Non-covalent)

P00.1: 18 residues within 4Å: Chain A: I.66, S.122, G.123, T.124, N.127, F.156, H.157, G.158, R.159, E.208, E.213, D.241, V.243, Q.244, K.270 Chain B: G.297, S.298, T.299 21 PLIP interactions: 12 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.156, A:E.208, A:V.243 Hydrogen bonds: A:G.123, A:T.124, A:N.127, A:Q.244, A:K.270, B:T.299, B:T.299 Water bridges: A:S.122, A:T.124, A:F.156, B:N.94, B:S.298, B:S.298, B:S.298, B:S.298, B:S.298, B:Y.300 Salt bridges: A:R.159 P00.17: 14 residues within 4Å: Chain B: S.122, G.123, T.124, N.127, F.156, H.157, G.158, R.159, E.208, E.213, D.241, V.243, Q.244, K.270 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.156, B:E.208, B:V.243 Hydrogen bonds: B:S.122, B:G.123, B:T.124, B:T.124, B:N.127, B:E.213, B:Q.244, B:K.270 Water bridges: B:E.208, B:K.270, A:N.121 Salt bridges: B:R.159, B:K.270 pi-Stacking: B:F.156

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 8 residues within 4Å: Chain A: S.93, V.95, F.96 Chain B: A.63, G.65, M.382, L.384 Ligands: EDO.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.95, B:L.384 Hydrogen bonds: A:S.93, A:S.93, B:G.65 ACT.8: 3 residues within 4Å: Chain A: I.183, I.184, H.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.185 Salt bridges: A:H.185 ACT.9: 3 residues within 4Å: Chain A: T.21, I.23 Chain B: R.103 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.103 ACT.10: 8 residues within 4Å: Chain A: V.95 Chain B: V.35, A.37, P.38, F.41, L.373, Y.374, A.377 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.95, B:V.35 Hydrogen bonds: B:Y.36 ACT.14: 3 residues within 4Å: Chain B: I.183, I.184, H.185 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.185 Salt bridges: B:H.185

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: G.72, H.73, C.74, H.75, L.78, G.274 Chain B: W.90 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:C.74, A:H.75 Water bridges: B:W.90 EDO.4: 9 residues within 4Å: Chain A: H.91, T.92, S.93, F.96 Chain B: D.61, G.65, H.73, M.382 Ligands: ACT.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.65, B:H.73, A:S.93, A:S.93 EDO.5: 3 residues within 4Å: Chain A: Y.137, E.286, I.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.137 Water bridges: A:T.284 EDO.6: 4 residues within 4Å: Chain A: S.143, K.146, D.200, H.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.200 Water bridges: A:D.200, A:D.200 EDO.11: 7 residues within 4Å: Chain A: W.90 Chain B: G.72, H.73, C.74, H.75, L.78, G.274 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.90, B:C.74, B:H.75 EDO.12: 3 residues within 4Å: Chain B: Y.137, E.286, I.287 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.284 EDO.13: 8 residues within 4Å: Chain A: F.28, I.32, Y.36 Chain B: N.94, T.97, N.98, A.101, G.302 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.97, B:G.301 Water bridges: A:Y.36 EDO.15: 5 residues within 4Å: Chain A: V.95 Chain B: I.66, L.384, N.385, R.392 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.385, B:N.385, B:R.392 EDO.16: 3 residues within 4Å: Chain B: S.143, D.200, H.201 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.143, B:D.200 Water bridges: B:S.143, B:K.146

1 x TNF: PICRIC ACID(Non-covalent)

TNF.7: 5 residues within 4Å: Chain A: K.45, K.47, W.52, G.56, E.58 2 PLIP interactions: 2 interactions with chain A pi-Stacking: A:W.52, A:W.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bisht, S. et al., Conformational transitions, ligand specificity and catalysis in N-acetylornithine aminotransferase: Implications on drug designing and rational enzyme engineering in omega aminotransferases. To be Published

Release Date

2014-03-26

Peptides

Acetylornithine/succinyldiaminopimelate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetylornithine/succinyldiaminopimelate aminotransferase

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