SMTL ID : 8apz.1

Crystal structure of wild-type L-N-Carbamoylase from Sinorhizobium meliloti

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 9 residues within 4Å: Chain A: H.108, D.119, G.120, E.153, H.215 Ligands: FE.2, ZN.3, FE.4, ORD.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.6 ZN.3: 8 residues within 4Å: Chain A: D.119, E.154, Q.218, H.407 Ligands: ZN.1, FE.2, FE.4, ORD.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.119, A:E.154, A:E.154, A:H.407 ZN.8: 9 residues within 4Å: Chain B: H.108, D.119, G.120, E.153, H.215 Ligands: FE.9, ZN.10, FE.11, ORD.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.108, B:D.119, B:H.215, H2O.14 ZN.10: 8 residues within 4Å: Chain B: D.119, E.154, Q.218, H.407 Ligands: ZN.8, FE.9, FE.11, ORD.12 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, ORD.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.6 FE.4: 8 residues within 4Å: Chain A: D.119, E.154, Q.218, H.407 Ligands: ZN.1, FE.2, ZN.3, ORD.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.119, A:E.154, A:E.154, A:H.407 FE.9: 9 residues within 4Å: Chain B: H.108, D.119, G.120, E.153, H.215 Ligands: ZN.8, ZN.10, FE.11, ORD.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.108, B:D.119, B:H.215, H2O.14 FE.11: 8 residues within 4Å: Chain B: D.119, E.154, Q.218, H.407 Ligands: ZN.8, FE.9, ZN.10, ORD.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.119, B:E.154, B:E.154, B:H.407

2 x ORD: D-ORNITHINE(Non-covalent)

ORD.5: 18 residues within 4Å: Chain A: H.108, D.119, E.153, E.154, A.161, H.215, Q.218, W.240, R.313, A.381, G.382, H.407 Chain B: H.251, N.300 Ligands: ZN.1, FE.2, ZN.3, FE.4 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.381 Hydrogen bonds: A:E.153, A:Q.218, A:G.382, B:N.300 Salt bridges: A:R.313, B:H.251 ORD.12: 18 residues within 4Å: Chain A: H.251, N.300 Chain B: H.108, D.119, E.153, E.154, A.161, H.215, Q.218, W.240, R.313, A.381, G.382, H.407 Ligands: ZN.8, FE.9, ZN.10, FE.11 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.381 Hydrogen bonds: B:E.153, B:Q.218, B:Q.218, B:G.382, B:G.382, A:N.300 Water bridges: B:H.383 Salt bridges: B:R.313, A:H.251

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain A: R.30, V.31, A.33, Y.372, A.419, D.423 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.33 Hydrogen bonds: A:V.31, A:V.31, A:Y.372 Water bridges: A:A.33 ACT.13: 4 residues within 4Å: Chain B: R.68, G.196, W.197, L.198 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.197 Water bridges: B:L.198 ACT.14: 5 residues within 4Å: Chain A: Q.275, M.279 Chain B: M.257, R.260, L.338 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.275 Hydrophobic interactions: B:L.338

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: R.29, K.369, H.427, E.431, I.435 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.29, A:R.29, A:K.369 GOL.15: 3 residues within 4Å: Chain B: M.273, E.330, I.334 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.330 Water bridges: B:M.273, B:E.330 GOL.16: 8 residues within 4Å: Chain A: P.296, N.297 Chain B: Q.57, P.113, A.156, R.157, P.183, Q.291 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:N.297, B:N.55 Hydrogen bonds: B:Q.57, B:Q.57, B:Q.291

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