SMTL ID : 8bpl.1

Aspartate transcarbamoylase mutant (N2045C, R2238C) from Chaetomium thermophilum CAD-like bound to carbamoyl phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-trimer

Ligands

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

CP.1: 15 residues within 4Å: Chain A: P.64, S.65, T.66, R.67, T.68, S.69, R.116, H.144, Q.147, P.277, L.278, P.279 Chain C: S.92, K.95 Ligands: SIN.8 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:S.65, A:T.66, A:R.67, A:R.67, A:T.68, A:T.68, A:T.68, A:R.116, A:Q.147, C:S.92, C:S.92 Water bridges: A:R.116, C:K.95 Salt bridges: A:R.67, A:R.116, C:K.95 CP.9: 15 residues within 4Å: Chain A: S.92, K.95 Chain B: P.64, S.65, T.66, R.67, T.68, S.69, R.116, H.144, Q.147, P.277, L.278, P.279 Ligands: SIN.16 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.65, B:T.66, B:R.67, B:R.67, B:T.68, B:T.68, B:T.68, B:R.116, B:Q.147, A:S.92, A:S.92 Water bridges: B:R.116, A:K.95 Salt bridges: B:R.67, B:R.116, A:K.95 CP.17: 15 residues within 4Å: Chain B: S.92, K.95 Chain C: P.64, S.65, T.66, R.67, T.68, S.69, R.116, H.144, Q.147, P.277, L.278, P.279 Ligands: SIN.24 16 PLIP interactions: 4 interactions with chain B, 12 interactions with chain C Hydrogen bonds: B:S.92, B:S.92, C:S.65, C:T.66, C:R.67, C:R.67, C:T.68, C:T.68, C:T.68, C:R.116, C:Q.147 Water bridges: B:K.95, C:R.116 Salt bridges: B:K.95, C:R.67, C:R.116

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.15, S.16, H.17, P.131, V.132, P.133 Ligand excluded by PLIP GOL.3: 9 residues within 4Å: Chain A: V.21, T.22, K.142, E.143, H.180, S.181, Y.184, V.207, Q.210 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: L.174, Y.175, A.200, L.201, E.243, R.244, F.245 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: L.159, L.165, D.233, K.269, T.271 Ligand excluded by PLIP GOL.6: 10 residues within 4Å: Chain A: T.59, L.60, F.61, S.69, P.85, I.86, Q.87 Chain C: P.85, Q.87, T.90 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: Y.62, E.63, V.93, H.117, P.118 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain B: K.15, S.16, H.17, P.131, V.132, P.133 Ligand excluded by PLIP GOL.11: 9 residues within 4Å: Chain B: V.21, T.22, K.142, E.143, H.180, S.181, Y.184, V.207, Q.210 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain B: L.174, Y.175, A.200, L.201, E.243, R.244, F.245 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain B: L.159, L.165, D.233, K.269, T.271 Ligand excluded by PLIP GOL.14: 10 residues within 4Å: Chain A: P.85, Q.87, T.90 Chain B: T.59, L.60, F.61, S.69, P.85, I.86, Q.87 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: Y.62, E.63, V.93, H.117, P.118 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain C: K.15, S.16, H.17, P.131, V.132, P.133 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain C: V.21, T.22, K.142, E.143, H.180, S.181, Y.184, V.207, Q.210 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain C: L.174, Y.175, A.200, L.201, E.243, R.244, F.245 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain C: L.159, L.165, D.233, K.269, T.271 Ligand excluded by PLIP GOL.22: 10 residues within 4Å: Chain B: P.85, Q.87, T.90 Chain C: T.59, L.60, F.61, S.69, P.85, I.86, Q.87 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain C: Y.62, E.63, V.93, H.117, P.118 Ligand excluded by PLIP

3 x SIN: SUCCINIC ACID(Non-covalent)

SIN.8: 10 residues within 4Å: Chain A: H.144, G.176, P.178, T.238, R.239, H.276, P.277, L.278, P.279 Ligands: CP.1 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:P.178, A:P.277 Hydrogen bonds: A:R.239 Water bridges: A:R.239, A:R.239, A:R.239, C:K.95 Salt bridges: A:H.276, C:K.95 SIN.16: 10 residues within 4Å: Chain B: H.144, G.176, P.178, T.238, R.239, H.276, P.277, L.278, P.279 Ligands: CP.9 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.178, B:P.277 Hydrogen bonds: B:R.239 Water bridges: B:R.239, B:R.239, B:R.239, A:K.95 Salt bridges: B:H.276, A:K.95 SIN.24: 10 residues within 4Å: Chain C: H.144, G.176, P.178, T.238, R.239, H.276, P.277, L.278, P.279 Ligands: CP.17 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:P.178, C:P.277 Hydrogen bonds: C:R.239 Water bridges: C:R.239, C:R.239, C:R.239, B:K.95 Salt bridges: C:H.276, B:K.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Del Cano-Ochoa, F. et al., A Tailored Strategy to Crosslink the Aspartate Transcarbamoylase Domain of the Multienzymatic Protein CAD. Molecules (2023)

Release Date

2023-02-01

Peptides

Carbamoyl-phosphate synthase (glutamine-hydrolyzing): ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Carbamoyl-phosphate synthase (glutamine-hydrolyzing)