SMTL ID : 8qeu.1

Crystal structure of ornithine transcarbamylase from Arabidopsis thaliana (AtOTC) in complex with ornithine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

4 x ORN: L-ornithine(Non-covalent)

ORN.1: 11 residues within 4Å: Chain A: L.145, N.180, N.181, D.242, S.246, M.247, C.282, L.283, P.284 Ligands: SO4.5, NA.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.181, A:N.181, A:D.242, A:M.247, A:L.283 ORN.12: 12 residues within 4Å: Chain B: L.145, H.150, N.180, N.181, M.182, D.242, V.243, C.282, L.283, P.284 Ligands: SO4.16, NA.18 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.145 Hydrogen bonds: B:N.181, B:N.181, B:L.283 Water bridges: B:R.123, B:N.180, B:N.180 ORN.19: 11 residues within 4Å: Chain C: L.145, N.180, N.181, D.242, S.246, M.247, C.282, L.283, P.284 Ligands: SO4.23, NA.29 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.145 Hydrogen bonds: C:N.181, C:N.181, C:D.242, C:M.247, C:L.283 ORN.22: 5 residues within 4Å: Chain C: L.48, E.53, R.54, N.55, Y.56 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.48, C:E.53 Hydrogen bonds: C:E.53, C:R.54, C:N.55, C:N.55, C:Y.56 Water bridges: C:N.55

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: Q.275, K.276, Y.278, P.299, Y.300 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.278, A:Y.278 PEG.13: 6 residues within 4Å: Chain B: Q.275, K.276, A.277, Y.278, P.299, Y.300 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.299 PEG.20: 5 residues within 4Å: Chain C: Q.275, K.276, Y.278, P.299, Y.300 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Y.278, C:Y.278

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

EDO.3: 4 residues within 4Å: Chain A: M.247, G.248, Q.249, K.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.248, A:G.248, A:K.250 Water bridges: A:D.251 EDO.6: 3 residues within 4Å: Chain A: L.21, H.320, L.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.21, A:L.21 Water bridges: A:G.323 EDO.7: 2 residues within 4Å: Chain A: K.46, E.163 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.46 EDO.8: 4 residues within 4Å: Chain A: R.111, S.114, R.115 Chain B: F.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.111, A:R.115 Water bridges: A:S.114 EDO.9: 2 residues within 4Å: Chain A: L.25, D.29 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.29, A:D.29 EDO.14: 4 residues within 4Å: Chain B: R.111, S.114, R.115 Chain C: F.304 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.111, B:R.115 Water bridges: B:S.114 EDO.15: 3 residues within 4Å: Chain B: L.25, D.29, L.131 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.29 EDO.17: 3 residues within 4Å: Chain B: L.21, H.320, L.321 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.21, B:H.320 Water bridges: B:G.323 EDO.21: 4 residues within 4Å: Chain A: F.304 Chain C: R.111, S.114, R.115 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.111, C:R.115 Water bridges: C:R.111, C:S.114 EDO.26: 2 residues within 4Å: Chain C: L.21, H.320 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.320 EDO.27: 3 residues within 4Å: Chain C: E.44, L.48, Y.56 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.44 Water bridges: C:K.41, C:Y.56 EDO.28: 2 residues within 4Å: Chain C: L.25, D.29 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.29, C:D.29

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

SO4.4: 3 residues within 4Å: Chain A: H.89 Chain B: H.89 Chain C: H.89 7 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Water bridges: C:G.88, C:H.89, A:H.89, B:H.89 Salt bridges: C:H.89, A:H.89, B:H.89 SO4.5: 9 residues within 4Å: Chain A: S.72, M.73, R.74, T.75, R.123, L.283 Chain C: R.103 Ligands: ORN.1, NA.11 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.72, A:M.73, A:R.74, A:T.75, A:L.283 Water bridges: A:R.310 Salt bridges: A:R.74, A:R.123, C:R.103 SO4.16: 8 residues within 4Å: Chain A: R.103 Chain B: S.72, M.73, R.74, T.75, L.283 Ligands: ORN.12, NA.18 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.72, B:M.73, B:R.74, B:T.75, B:L.283 Water bridges: B:T.75, B:R.310, A:R.103, A:R.103 Salt bridges: B:R.74, A:R.103 SO4.23: 8 residues within 4Å: Chain B: R.103 Chain C: S.72, M.73, R.74, T.75, L.283 Ligands: ORN.19, NA.29 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain C Salt bridges: B:R.103, C:R.74 Hydrogen bonds: C:S.72, C:M.73, C:R.74, C:T.75, C:L.283 Water bridges: C:R.310 SO4.24: 3 residues within 4Å: Chain A: K.60 Chain B: K.60 Chain C: K.60 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Water bridges: C:K.60, C:K.60 Salt bridges: C:K.60, A:K.60, B:K.60 SO4.25: 5 residues within 4Å: Chain C: I.162, E.163, H.164, I.165, G.166 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.163

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

NA.10: 5 residues within 4Å: Chain A: D.251, E.252, A.253, E.254, A.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.251, A:E.254, A:A.255 Water bridges: A:A.253 NA.11: 6 residues within 4Å: Chain A: T.75, R.123, H.150, R.310 Ligands: ORN.1, SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.123, A:H.150, A:R.310 NA.18: 5 residues within 4Å: Chain B: T.75, H.150, R.310 Ligands: ORN.12, SO4.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.150, B:R.310 Water bridges: B:T.75 NA.29: 5 residues within 4Å: Chain C: T.75, H.150, R.310 Ligands: ORN.19, SO4.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.75, C:R.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nielipinski, M. et al., Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae . Front Plant Sci (2023)

Release Date

2023-12-06

Peptides

Ornithine transcarbamylase, chloroplastic: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ornithine transcarbamylase, chloroplastic

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