SMTL ID : 5nc9.1

Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2,6-diamino-N-hydroxyhexanamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-tetramer

Ligands

4 x 8SZ: (2~{S})-2,6-bis(azanyl)-~{N}-oxidanyl-hexanamide(Non-covalent)

8SZ.1: 11 residues within 4Å: Chain A: D.50, D.51, H.100, H.104, P.140, Y.141, L.202, H.204, H.207 Chain D: H.243 Ligands: ZN.2 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:H.243, A:D.50, A:Y.141, A:H.207 8SZ.3: 12 residues within 4Å: Chain B: D.50, D.51, H.100, H.104, P.139, P.140, Y.141, W.165, W.172, L.202, H.204 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.141 Hydrogen bonds: B:Y.141 8SZ.7: 10 residues within 4Å: Chain B: H.243 Chain C: D.50, D.51, H.100, H.104, P.140, Y.141, H.204, H.207 Ligands: ZN.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.243, C:Y.141, C:H.207 8SZ.9: 12 residues within 4Å: Chain D: D.50, D.51, H.100, H.104, P.140, Y.141, G.142, W.165, W.172, L.202, H.204 Ligands: ZN.10 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.141 Hydrogen bonds: D:D.50, D:Y.141, D:G.142

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.51, H.100, H.104 Ligands: 8SZ.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.51, A:H.100, A:H.104 ZN.4: 4 residues within 4Å: Chain B: D.51, H.100, H.104 Ligands: 8SZ.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.2 ZN.8: 4 residues within 4Å: Chain C: D.51, H.100, H.104 Ligands: 8SZ.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.51, C:H.100, C:H.104 ZN.10: 4 residues within 4Å: Chain D: D.51, H.100, H.104 Ligands: 8SZ.9 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.51, D:H.100, D:H.104, H2O.4

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

CIT.5: 8 residues within 4Å: Chain B: W.165, T.166, I.167, D.168, N.193, F.241 Chain C: M.144, P.145 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.168, B:D.168, B:N.193

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: R.246 Chain B: E.59, P.208, A.212 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.208, A:R.246

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 9 residues within 4Å: Chain B: L.170, R.173, Y.174 Chain D: L.170, R.173, Y.174, N.175, K.176, M.177 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.176, D:M.177

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

Related Entries With Identical Sequence