SMTL ID : 4jez.1

N79R mutant of N-acetylornithine aminotransferase complexed with L-canaline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 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: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:W.90 Hydrogen bonds: A:C.74, A:H.75 EDO.3: 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: 9 residues within 4Å: Chain A: D.61, G.65, H.73, M.382 Chain B: H.91, T.92, S.93, F.96 Ligands: ACT.18 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.93, B:S.93, A:G.65, A:H.73 Water bridges: A:T.69 EDO.6: 4 residues within 4Å: Chain A: S.143, K.146, D.200, H.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.200 Water bridges: A:K.146 EDO.12: 8 residues within 4Å: Chain A: W.90 Chain B: T.69, G.72, H.73, C.74, H.75, L.78, G.274 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.74, B:H.75 Water bridges: A:W.90 EDO.14: 3 residues within 4Å: Chain B: S.143, D.200, H.201 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.143, B:D.200 Water bridges: B:K.146

10 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.3 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.384, A:V.95, A:F.96 Hydrogen bonds: B:G.65, B:I.66, A:S.93 Water bridges: B:V.383 ACT.4: 2 residues within 4Å: Chain A: K.45, W.52 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.45 ACT.7: 2 residues within 4Å: Chain A: K.148, I.184 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.184 Water bridges: A:K.148, A:K.148, A:K.148, A:D.182 Salt bridges: A:K.148 ACT.8: 4 residues within 4Å: Chain A: Y.137, H.142, Q.235, L.237 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.137, A:L.237 Water bridges: A:C.231, A:Q.235, A:Q.235 Salt bridges: A:H.142 ACT.10: 3 residues within 4Å: Chain A: T.220, P.221, E.222 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.222 Hydrogen bonds: A:E.222 Water bridges: A:T.220 ACT.13: 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 ACT.15: 4 residues within 4Å: Chain B: Y.137, H.142, Q.235, L.237 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.237 Hydrogen bonds: B:Y.137, B:Y.137, B:Q.235 Water bridges: B:Q.235 Salt bridges: B:H.142 ACT.17: 8 residues within 4Å: Chain A: V.95, F.96 Chain B: A.37, P.38, F.41, L.373, Y.374, A.377 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.37, A:V.95, A:F.96 ACT.18: 8 residues within 4Å: Chain A: A.63, G.65, M.382, L.384 Chain B: S.93, V.95, F.96 Ligands: EDO.5 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.384, B:V.95, B:F.96 Hydrogen bonds: A:G.65, B:S.93 ACT.20: 3 residues within 4Å: Chain B: T.220, P.221, E.222 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.222 Hydrogen bonds: B:T.220, B:E.222 Water bridges: B:E.222

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: I.109, T.112, F.113, A.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.109 NA.19: 4 residues within 4Å: Chain B: I.109, T.112, F.113, A.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.109

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

P00.11: 15 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 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:E.208, A:V.243 Hydrogen bonds: A:G.123, A:T.124, A:N.127, A:Q.244, A:K.270 Water bridges: A:T.124, A:E.208, A:K.270, B:N.121 pi-Stacking: A:F.156 P00.16: 15 residues within 4Å: Chain B: 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 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.156, B:E.208, B:V.243 Hydrogen bonds: B:G.123, B:T.124, B:T.124, B:N.127, B:Q.244, B:K.270 Water bridges: B:S.122, B:E.208 pi-Stacking: B:F.156 Salt bridges: A:R.94

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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