SMTL ID : 8qev.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-trimer

Ligands

3 x CP: PHOSPHORIC ACID MONO(FORMAMIDE)ESTER(Non-covalent)

CP.1: 11 residues within 4Å: Chain A: S.72, M.73, R.74, T.75, R.123, H.150, Q.153, C.282, L.283, R.310 Chain C: R.103 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:M.73, A:R.74, A:T.75, A:T.75, A:R.123, A:Q.153, A:R.310 Salt bridges: A:R.74, A:R.123, C:R.103 Water bridges: C:R.103 CP.13: 11 residues within 4Å: Chain A: R.103 Chain B: S.72, M.73, R.74, T.75, R.123, H.150, Q.153, C.282, L.283, R.310 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.73, B:R.74, B:T.75, B:T.75, B:R.123, B:Q.153, B:R.310 Salt bridges: B:R.74, B:R.123, A:R.103 Water bridges: A:R.103 CP.24: 11 residues within 4Å: Chain B: R.103 Chain C: S.72, M.73, R.74, T.75, R.123, H.150, Q.153, C.282, L.283, R.310 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:M.73, C:R.74, C:T.75, C:T.75, C:R.123, C:Q.153, C:R.310 Salt bridges: C:R.74, C:R.123, B:R.103 Water bridges: B:R.103

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

EDO.2: 6 residues within 4Å: Chain A: H.148, D.208, E.210, R.211, K.214 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.208, A:R.211 Water bridges: A:E.210 EDO.4: 2 residues within 4Å: Chain A: Q.128, L.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.128 EDO.5: 3 residues within 4Å: Chain A: E.163, H.164, G.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.164 EDO.7: 3 residues within 4Å: Chain A: H.127, H.148 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.148 EDO.11: 3 residues within 4Å: Chain A: R.115 Chain B: H.164, P.305 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.164, A:R.115, A:R.115 EDO.15: 4 residues within 4Å: Chain B: K.216, I.223, E.224, I.225 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.216, B:K.216, B:I.225, B:I.225 EDO.22: 4 residues within 4Å: Chain B: E.163, H.164, I.165, G.166 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.162, B:G.166 EDO.23: 3 residues within 4Å: Chain A: R.287, N.293 Chain C: R.107 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Water bridges: A:N.293, A:N.293, A:N.293 Hydrogen bonds: C:R.107, C:R.107 EDO.26: 4 residues within 4Å: Chain C: E.163, H.164, I.165, G.166 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.165 EDO.28: 6 residues within 4Å: Chain A: Y.92 Chain B: D.97 Chain C: Y.92, G.94, D.97 Ligands: EDO.33 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:D.97, C:G.94, C:D.97 Water bridges: B:N.96, C:Y.92, C:N.96 EDO.29: 4 residues within 4Å: Chain C: V.212, K.216, E.224, I.225 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.216, C:I.225 Water bridges: C:K.209, C:K.209 EDO.30: 3 residues within 4Å: Chain C: Q.99, M.100, K.102 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.99 Water bridges: C:M.100 EDO.33: 6 residues within 4Å: Chain A: Y.92, P.95, N.96 Chain C: N.96, D.97 Ligands: EDO.28 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.96, C:D.97, A:Y.92, A:N.96 Water bridges: C:N.96, C:D.97, A:N.96

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 6 residues within 4Å: Chain A: Q.275, K.276, A.277, Y.278, P.299, Y.300 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.278, A:Y.278 PGE.25: 5 residues within 4Å: Chain C: Q.275, K.276, Y.278, P.299, Y.300 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Y.278

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

PEG.6: 2 residues within 4Å: Chain A: E.163, H.164 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.46, A:K.46, A:K.46 PEG.14: 5 residues within 4Å: Chain B: Q.275, K.276, Y.278, P.299, Y.300 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.299 Water bridges: B:K.276, B:Y.278, B:Y.278 PEG.16: 3 residues within 4Å: Chain B: K.172, H.196, E.231 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.196, B:E.231, B:E.231 PEG.27: 2 residues within 4Å: Chain C: L.48, Y.56 No protein-ligand interaction detected (PLIP)

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

SO4.8: 3 residues within 4Å: Chain A: H.89 Chain B: H.89 Chain C: H.89 8 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 3 interactions with chain B Water bridges: C:G.88, C:H.89, A:H.89, B:H.89, B:H.89 Salt bridges: C:H.89, A:H.89, B:H.89 SO4.9: 3 residues within 4Å: Chain A: D.266, E.267, T.292 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.267, A:T.292 Water bridges: A:A.268, A:N.293, A:G.294 SO4.10: 3 residues within 4Å: Chain A: R.111, R.115 Chain B: F.304 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.111, A:R.111, A:R.115 Salt bridges: A:R.115 SO4.17: 3 residues within 4Å: Chain B: R.111, R.115 Chain C: F.304 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.111, B:R.111, B:R.115 Salt bridges: B:R.115 SO4.18: 2 residues within 4Å: Chain B: K.60 Chain C: K.60 9 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C, 4 interactions with chain B Water bridges: A:K.60, C:K.60, C:K.60, B:K.60, B:K.60, B:K.60 Salt bridges: A:K.60, C:K.60, B:K.60 SO4.19: 2 residues within 4Å: Chain B: R.115 Chain C: P.305 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.115 Water bridges: C:H.164 SO4.20: 3 residues within 4Å: Chain B: D.266, E.267, T.292 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.267, B:T.292, B:T.292 Water bridges: B:A.268, B:N.293, B:G.294 SO4.21: 4 residues within 4Å: Chain B: K.41, V.45, L.48, Y.56 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.41 SO4.31: 3 residues within 4Å: Chain A: F.304 Chain C: R.111, R.115 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.111, C:R.111 Salt bridges: C:R.115 SO4.32: 3 residues within 4Å: Chain C: D.266, E.267, T.292 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.267, C:T.292, C:T.292 Water bridges: C:A.268, C:G.294

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

NA.12: 3 residues within 4Å: Chain A: D.118, V.139, L.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.118 Water bridges: A:D.118

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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