SMTL ID : 5o6y.4 (3 other biounits)

Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: F.35, H.179, L.180, Q.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.180, A:Q.181 Water bridges: A:G.182

1 x 5YA: 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide(Non-covalent)

5YA.2: 11 residues within 4Å: Chain A: D.28, D.29, H.79, H.83, X.119, Y.120, W.141, L.171, H.173 Ligands: ZN.3, PEG.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.120, A:W.141, A:L.171 Water bridges: A:Y.120, A:Y.120

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.28, D.29, H.79, H.83, X.119 Ligands: 5YA.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.29, A:H.79, A:H.83 ZN.8: 2 residues within 4Å: Chain A: H.46, K.195 No protein-ligand interaction detected (PLIP)

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: H.46, N.47, K.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.195 Water bridges: A:N.47 PEG.5: 7 residues within 4Å: Chain A: T.2, Y.12, F.14, G.121, Q.140, W.141 Ligands: 5YA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.2, A:Y.12 PEG.6: 7 residues within 4Å: Chain A: S.15, S.142, V.143, N.163, F.165, S.168 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.142, A:S.142

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 5 residues within 4Å: Chain A: S.15, G.16, P.166, G.167 Ligands: PEG.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.15, A:G.16

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

CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fadouloglou, V.E. et al., Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide. To Be Published

Release Date

2018-06-20

Peptides

Peptidoglycan N-acetylglucosamine deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Peptidoglycan N-acetylglucosamine deacetylase

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