SMTL ID : 5o6y.3 (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

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

SO4.1: 5 residues within 4Å: Chain A: H.46, I.191, P.192, K.195 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.45, A:Q.45, A:H.46 Salt bridges: A:H.46, A:K.195 SO4.2: 3 residues within 4Å: Chain A: H.179, L.180, Q.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.179, A:L.180, A:Q.181 Water bridges: A:G.182 SO4.3: 3 residues within 4Å: Chain A: N.47, K.195 Ligands: SO4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.47 Water bridges: A:H.46 Salt bridges: A:K.195 SO4.4: 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

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

5YA.5: 9 residues within 4Å: Chain A: D.28, D.29, H.79, H.83, X.119, Y.120, W.148, H.173 Ligands: ZN.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.120, A:Y.120 Hydrogen bonds: A:D.28, A:H.83 Water bridges: A:Y.120, A:Y.120 pi-Stacking: A:W.148, A:W.148

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: D.28, D.29, H.79, H.83, X.119 Ligands: 5YA.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.29, A:H.79, A:H.83

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

PE3.7: 5 residues within 4Å: Chain A: S.142, V.143, D.144, N.159, N.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.144, A:N.159

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

PEG.8: 4 residues within 4Å: Chain A: F.14, G.121, Q.140, W.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.121 Water bridges: A:T.2 PEG.9: 9 residues within 4Å: Chain A: S.15, S.142, V.143, N.163, F.165, P.166, G.167, S.168 Ligands: NA.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.143, A:F.165 Hydrogen bonds: A:S.142

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

NA.10: 1 residues within 4Å: Chain A: S.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.206 Water bridges: A:S.206 NA.11: 2 residues within 4Å: Chain A: S.152, T.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.152, A:T.155, A:T.155 NA.12: 1 residues within 4Å: Chain A: S.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.211 NA.13: 5 residues within 4Å: Chain A: S.15, G.16, P.166, G.167 Ligands: PEG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.16 Water bridges: A:Y.18

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
C

Peptidoglycan N-acetylglucosamine deacetylase

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