SMTL ID : 5o6y.1 (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

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: P.17, Y.18, N.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.18, A:N.19 SO4.2: 3 residues within 4Å: Chain A: 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 SO4.3: 3 residues within 4Å: Chain A: S.211, K.212, E.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.211, A:K.212

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

5YA.4: 11 residues within 4Å: Chain A: D.28, D.29, H.79, H.83, Y.120, W.141, D.144, W.148, L.171, H.173 Ligands: PEG.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.141, A:L.171 Hydrogen bonds: A:H.79 pi-Cation interactions: A:H.173

1 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)

PE3.5: 4 residues within 4Å: Chain A: F.14, Q.140, W.141 Ligands: PEG.8 No protein-ligand interaction detected (PLIP)

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

PEG.6: 2 residues within 4Å: Chain A: N.19, K.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19 PEG.7: 6 residues within 4Å: Chain A: W.1, W.6, E.122, I.123, L.124, E.125 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.1, A:E.122, A:E.122, A:E.125 Water bridges: A:N.126 PEG.8: 6 residues within 4Å: Chain A: W.1, Y.120, G.121, E.122 Ligands: 5YA.4, PE3.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.1 Hydrogen bonds: A:Y.120

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.9: 4 residues within 4Å: Chain A: V.89, N.90, E.91, L.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.91

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

NA.10: 2 residues within 4Å: Chain A: S.142, S.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.142, A:S.142 Water bridges: A:S.15 NA.11: 2 residues within 4Å: Chain A: F.14, S.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.15, A:S.15 Water bridges: A:F.14 NA.12: 2 residues within 4Å: Chain A: S.15, G.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.15 Water bridges: A:S.15 NA.13: 2 residues within 4Å: Chain A: F.165, P.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.166 NA.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.15: 1 residues within 4Å: Chain A: W.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.130 Water bridges: A:Q.134 NA.16: 3 residues within 4Å: Chain A: W.1, P.3, Y.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.1, A:Y.12

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

CL.17: 2 residues within 4Å: Chain A: T.210, S.211 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
A

Peptidoglycan N-acetylglucosamine deacetylase