SMTL ID : 5nel.1

Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with ThiametG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.50, D.51, H.100, H.104 Ligands: ACT.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.51, A:H.100, A:H.104, H2O.1, ACT.2 ZN.3: 4 residues within 4Å: Chain B: D.51, H.100, H.104 Ligands: NHT.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.51, B:H.100, B:H.104 ZN.7: 5 residues within 4Å: Chain C: D.50, D.51, H.100, H.104 Ligands: ACT.8 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.2, ACT.8 ZN.9: 4 residues within 4Å: Chain D: D.51, H.100, H.104 Ligands: NHT.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.51, D:H.100, D:H.104

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

ACT.2: 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.1 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.8: 9 residues within 4Å: Chain B: H.243 Chain C: D.50, H.100, H.104, P.140, Y.141, L.202, H.204 Ligands: ZN.7 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.202 Hydrogen bonds: C:D.50, C:Y.141 Salt bridges: C:H.100, C:H.104, C:H.204

2 x NHT: (3AR,5R,6S,7R,7AR)-2-(ETHYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL

NHT.4: 8 residues within 4Å: Chain B: D.50, D.51, H.100, H.104, Y.141, L.202, H.204 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.50 NHT.10: 9 residues within 4Å: Chain D: D.50, D.51, H.100, H.104, Y.141, W.172, L.202, H.204 Ligands: ZN.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.50

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

PGE.5: 12 residues within 4Å: Chain B: L.170, R.173, Y.174, N.175, K.176, M.177 Chain D: L.170, R.173, Y.174, N.175, K.176, M.177 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.173, B:N.175, B:K.176, D:N.175, D:K.176

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

EDO.6: 4 residues within 4Å: Chain B: T.166, I.167, D.168, N.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.168, B:N.193

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

CIT.11: 7 residues within 4Å: Chain A: M.144 Chain B: K.176 Chain D: T.166, I.167, D.168, L.170, N.193 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.165, D:D.168, D:D.168, D: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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