SMTL ID : 5ncd.1

Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2-amino-5-(diaminomethylideneamino)-N-hydroxypentanamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

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

ACT.1: 9 residues within 4Å: Chain A: D.50, D.51, H.100, H.104, P.140, Y.141, H.204 Chain D: H.243 Ligands: ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.50, A:Y.141 Salt bridges: A:H.100, A:H.104, A:H.204 ACT.6: 9 residues within 4Å: Chain B: H.243 Chain C: D.50, D.51, H.100, H.104, P.140, Y.141, H.204 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.141 Salt bridges: C:H.100, C:H.104, C:H.204 ACT.8: 8 residues within 4Å: Chain D: D.50, H.100, H.104, P.139, P.140, Y.141, H.204 Ligands: ZN.9 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.50, D:Y.141 Salt bridges: D:H.100, D:H.104, D:H.204

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.51, H.100, H.104 Ligands: ACT.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.51, A:H.100, A:H.104, ACT.1 ZN.4: 4 residues within 4Å: Chain B: D.51, H.100, H.104 Ligands: AHL.3 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.51, B:H.100, B:H.104, H2O.3 ZN.7: 5 residues within 4Å: Chain C: D.50, D.51, H.100, H.104 Ligands: ACT.6 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:D.51, C:H.100, C:H.104, H2O.4, ACT.6 ZN.9: 4 residues within 4Å: Chain D: D.51, H.100, H.104 Ligands: ACT.8 5 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:D.51, D:H.100, D:H.104, H2O.5, ACT.8

1 x AHL: N-HYDROXY-L-ARGININAMIDE(Non-covalent)

AHL.3: 11 residues within 4Å: Chain B: D.50, D.51, H.100, H.104, P.140, Y.141, W.165, W.172, L.202, H.204 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.141 Water bridges: B:H.204

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 7 residues within 4Å: Chain B: W.165, T.166, I.167, D.168, N.193, F.241 Chain C: M.144 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.166, B:D.168, B:N.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giastas, P. et al., Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors. Biochemistry (2018)

Release Date

2018-02-21

Peptides

Peptidoglycan N-acetylglucosamine deacetylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Peptidoglycan N-acetylglucosamine deacetylase

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