SMTL ID : 4jex.1

Y21K mutant of N-acetylornithine aminotransferase complexed with L-canaline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

8 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 Hydrogen bonds: B:W.90, A:C.74, A:H.75 EDO.2: 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.15 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.65, A:H.73, B:S.93, B:S.93 Water bridges: A:T.69 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.4 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.7: 4 residues within 4Å: Chain A: Y.137, E.286, I.287 Ligands: ACT.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.137 Water bridges: A:T.284 EDO.8: 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.13: 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: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.74, B:H.75 Water bridges: A:W.90 EDO.18: 3 residues within 4Å: Chain B: Y.137, E.286, I.287 No protein-ligand interaction detected (PLIP) EDO.22: 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

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

ACT.4: 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 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.384, A:V.95 Hydrogen bonds: B:G.65, A:S.93 Water bridges: B:V.383 ACT.5: 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, A:F.223 ACT.6: 5 residues within 4Å: Chain A: Y.137, H.142, Q.235, L.237 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.137, A:L.237 Water bridges: A:C.231, A:Q.235 Salt bridges: A:H.142 ACT.10: 6 residues within 4Å: Chain A: M.120, E.125, E.128 Chain B: T.124, R.159, S.160 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:S.122, B:R.159, B:R.159, A:K.132 Hydrophobic interactions: A:E.125, A:E.128 Hydrogen bonds: A:E.125 ACT.11: 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.14: 3 residues within 4Å: Chain B: T.220, P.221, E.222 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.222 Hydrogen bonds: B:T.220, B:E.222, B:E.222, B:F.223 ACT.15: 8 residues within 4Å: Chain A: A.63, G.65, M.382, L.384 Chain B: S.93, V.95, F.96 Ligands: EDO.2 6 PLIP interactions: 3 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 Water bridges: A:V.383 ACT.16: 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: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.95, A:F.96, B:A.37 ACT.17: 6 residues within 4Å: Chain B: E.360, L.361, K.362, P.363, K.366, D.389 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.363 Hydrogen bonds: B:E.360 Salt bridges: B:K.366 ACT.19: 5 residues within 4Å: Chain A: T.124, R.159, S.160 Chain B: E.125, E.128 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.128 Hydrogen bonds: B:E.125, A:T.124 Water bridges: B:T.129, A:S.122, A:R.159, A:R.159 ACT.21: 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

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

P00.9: 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.156, A:E.208, A:V.243 Hydrogen bonds: A:G.123, A:T.124, A:N.127, A:E.213, A:Q.244, A:K.270 Water bridges: A:N.121, A:T.124, A:T.124, A:K.270 P00.24: 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 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:E.208, B:V.243 Hydrogen bonds: B:G.123, B:T.124, B:T.124, B:N.127, B:E.213, B:Q.244, B:K.270 Water bridges: B:N.121, B:S.122, B:E.208, B:K.270 Salt bridges: B:R.159 pi-Stacking: B:F.156

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

NA.12: 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.23: 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:T.112

1 x TNF: PICRIC ACID(Non-covalent)

TNF.20: 6 residues within 4Å: Chain B: L.33, P.34, V.35, K.36, R.370, Y.374 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.34 pi-Cation interactions: B:K.36

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