SMTL ID : 4h31.1

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoyl phosphate and L-norvaline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

3 x NVA: NORVALINE(Non-covalent)

NVA.1: 9 residues within 4Å: Chain A: L.154, H.159, N.192, N.193, D.257, S.261, M.262, L.300 Ligands: CP.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.154 Hydrogen bonds: A:N.193, A:D.257, A:M.262 Water bridges: A:N.193 NVA.14: 10 residues within 4Å: Chain B: L.154, H.159, N.192, N.193, V.194, D.257, S.261, M.262, L.300 Ligands: CP.15 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.154, B:V.194 Hydrogen bonds: B:N.193, B:D.257, B:M.262 Water bridges: B:N.193 NVA.25: 8 residues within 4Å: Chain C: L.154, N.192, N.193, D.257, S.261, M.262, L.300 Ligands: CP.27 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.154 Hydrogen bonds: C:N.193, C:D.257, C:M.262

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

CP.2: 12 residues within 4Å: Chain A: S.81, T.82, R.83, T.84, R.132, H.159, Q.162, C.299, L.300, R.344 Chain B: Q.108 Ligands: NVA.1 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.82, A:R.83, A:T.84, A:T.84, A:R.132, A:Q.162, A:R.344, B:Q.108 Water bridges: A:Q.162 Salt bridges: A:R.83, A:R.132 CP.15: 12 residues within 4Å: Chain B: S.81, T.82, R.83, T.84, R.132, H.159, Q.162, C.299, L.300, R.344 Chain C: Q.108 Ligands: NVA.14 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.82, B:R.83, B:T.84, B:T.84, B:R.132, B:Q.162, B:R.344, C:Q.108 Salt bridges: B:R.83, B:R.132 CP.27: 12 residues within 4Å: Chain A: Q.108 Chain C: S.81, T.82, R.83, T.84, R.132, H.159, Q.162, C.299, L.300, R.344 Ligands: NVA.25 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.82, C:R.83, C:T.84, C:T.84, C:R.132, C:Q.162, C:R.344, A:Q.108 Water bridges: C:Q.162 Salt bridges: C:R.83, C:R.132

3 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.3: 5 residues within 4Å: Chain A: E.331 Chain B: K.116, R.120, A.144, F.145 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.331, B:R.120 Water bridges: B:R.120 PE5.23: 6 residues within 4Å: Chain B: D.156, E.157, R.191, M.262, G.263, E.264 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.156, B:D.156, B:N.196 PE5.28: 5 residues within 4Å: Chain C: D.156, R.191, M.262, G.263, E.264 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.191

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

PEG.4: 3 residues within 4Å: Chain A: N.31, A.144, G.147 Ligand excluded by PLIP PEG.5: 5 residues within 4Å: Chain A: D.156, R.191, M.262, G.263, E.264 Ligand excluded by PLIP PEG.6: 6 residues within 4Å: Chain A: L.286, K.287, G.290, N.291, P.292, H.334 Ligand excluded by PLIP PEG.8: 4 residues within 4Å: Chain A: D.208, R.210, T.239, E.246 Ligand excluded by PLIP PEG.9: 3 residues within 4Å: Chain A: N.284, K.287, Q.288 Ligand excluded by PLIP PEG.10: 4 residues within 4Å: Chain A: K.277, P.278, Q.280, N.282 Ligand excluded by PLIP PEG.12: 5 residues within 4Å: Chain A: R.120 Chain C: F.330, E.331, S.335, F.338 Ligand excluded by PLIP PEG.13: 2 residues within 4Å: Chain A: D.50, D.54 Ligand excluded by PLIP PEG.16: 3 residues within 4Å: Chain B: K.277, F.318, M.320 Ligand excluded by PLIP PEG.18: 6 residues within 4Å: Chain B: L.286, K.287, G.290, N.291, P.292, H.334 Ligand excluded by PLIP PEG.20: 6 residues within 4Å: Chain A: D.306, E.307, T.308, T.309, K.312 Chain B: G.110 Ligand excluded by PLIP PEG.21: 6 residues within 4Å: Chain B: A.180, D.181, I.182, G.206, D.208, G.235 Ligand excluded by PLIP PEG.22: 5 residues within 4Å: Chain B: A.53, K.56, K.57, L.168, E.172 Ligand excluded by PLIP PEG.24: 4 residues within 4Å: Chain B: S.41, T.42, K.204, I.230 Ligand excluded by PLIP PEG.29: 4 residues within 4Å: Chain C: R.210, T.239, E.246, Q.249 Ligand excluded by PLIP PEG.30: 6 residues within 4Å: Chain C: L.286, K.287, G.290, N.291, P.292, H.334 Ligand excluded by PLIP PEG.31: 1 residues within 4Å: Chain C: E.331 Ligand excluded by PLIP PEG.33: 4 residues within 4Å: Chain C: S.261, M.262, G.263, E.264 Ligand excluded by PLIP

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain A: K.36, L.37, F.158, P.160, S.197 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: N.282, M.283, T.326, E.328 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain B: K.36, L.37, F.158, P.160, S.197 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: N.282, M.283, T.326, E.328 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain C: K.36, L.37, F.158, P.160, S.197 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain C: N.282, M.283, T.326, E.328 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shabalin, I.G. et al., Structural studies of ornithine carbamoyltransferase from various pathogens. To be Published

Release Date

2012-09-26

Peptides

Ornithine carbamoyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ornithine carbamoyltransferase

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