SMTL ID : 8aq0.1

Crystal structure of L-N-Carbamoylase from Sinorhizobium meliloti mutant L217G/F329C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: H.108, D.119, E.153, H.215 Ligands: FE.2, ZN.3, FE.4, NV6.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.108, A:D.119, A:H.215, H2O.2 ZN.3: 8 residues within 4Å: Chain A: D.119, E.154, Q.218, H.407 Ligands: ZN.1, FE.2, FE.4, NV6.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.119, A:E.154, A:E.154, A:H.407 ZN.6: 9 residues within 4Å: Chain B: H.108, D.119, G.120, E.153, H.215 Ligands: FE.7, ZN.8, FE.9, NV6.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.108, B:D.119, B:H.215, H2O.4 ZN.8: 8 residues within 4Å: Chain B: D.119, E.154, Q.218, H.407 Ligands: ZN.6, FE.7, FE.9, NV6.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.119, B:E.154, B:E.154, B:H.407

4 x FE: FE (III) ION(Non-covalent)

FE.2: 9 residues within 4Å: Chain A: H.108, D.119, G.120, E.153, H.215 Ligands: ZN.1, ZN.3, FE.4, NV6.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.108, A:D.119, A:H.215, H2O.2 FE.4: 8 residues within 4Å: Chain A: D.119, E.154, Q.218, H.407 Ligands: ZN.1, FE.2, ZN.3, NV6.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.119, A:E.154, A:E.154, A:H.407 FE.7: 9 residues within 4Å: Chain B: H.108, D.119, G.120, E.153, H.215 Ligands: ZN.6, ZN.8, FE.9, NV6.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.108, B:D.119, B:H.215, H2O.4 FE.9: 8 residues within 4Å: Chain B: D.119, E.154, Q.218, H.407 Ligands: ZN.6, FE.7, ZN.8, NV6.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.119, B:E.154, B:E.154, B:H.407

2 x NV6: (2~{S})-2-(aminocarbonylamino)-3-(4-hydroxyphenyl)propanoic acid(Non-covalent)

NV6.5: 20 residues within 4Å: Chain A: H.108, D.119, E.153, E.154, A.161, M.162, H.215, Q.218, W.240, R.313, A.381, G.382, H.383, H.407 Chain B: H.251, N.300 Ligands: ZN.1, FE.2, ZN.3, FE.4 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:N.300, A:Q.218, A:Q.218, A:W.240, A:G.382, A:G.382 Salt bridges: B:H.251, A:R.313, A:H.407 Hydrophobic interactions: A:A.161, A:W.240 pi-Cation interactions: A:R.313 NV6.10: 20 residues within 4Å: Chain A: H.251, N.300 Chain B: H.108, D.119, E.153, E.154, A.161, M.162, H.215, Q.218, W.240, R.313, A.381, G.382, H.383, H.407 Ligands: ZN.6, FE.7, ZN.8, FE.9 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.161, B:W.240 Hydrogen bonds: B:Q.218, B:G.238, B:G.382, B:G.382, B:G.382, A:N.300 Salt bridges: B:R.313, B:H.407, A:H.251 pi-Cation interactions: B:R.313

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

CL.11: 3 residues within 4Å: Chain B: T.60, D.61, R.194 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rubini, R. et al., Selecting Better Biocatalysts by Complementing Recoded Bacteria. Angew.Chem.Int.Ed.Engl. (2023)

Release Date

2022-11-16

Peptides

N-carbamoyl-L-amino-acid hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-carbamoyl-L-amino-acid hydrolase