SMTL ID : 8jqf.1

Structure of CmCBDA in complex with Ni2+ and Glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: D.25, E.81, W.82, H.146, M.147, H.233, F.251, R.256 Ligands: NI.2, SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.81, A:E.81, A:R.256 Water bridges: A:H.248, A:N.250 GOL.4: 10 residues within 4Å: Chain B: D.25, E.81, W.82, H.146, M.147, H.233, F.251, R.256 Ligands: NI.5, SO4.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.25, B:E.81, B:R.256 Water bridges: B:H.248, B:N.250

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 5 residues within 4Å: Chain A: D.25, H.75, H.146 Ligands: GOL.1, SO4.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.25, A:H.75, A:H.146 NI.5: 5 residues within 4Å: Chain B: D.25, H.75, H.146 Ligands: GOL.4, SO4.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.25, B:H.75, B:H.146

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

SO4.3: 9 residues within 4Å: Chain A: D.24, D.25, H.75, S.145, H.146, M.147, H.233 Ligands: GOL.1, NI.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.24, A:M.147 Salt bridges: A:H.75, A:H.146, A:H.233 SO4.6: 10 residues within 4Å: Chain B: D.24, D.25, H.75, S.145, H.146, M.147, M.201, H.233 Ligands: GOL.4, NI.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.24, B:S.145, B:M.147 Water bridges: B:Y.148 Salt bridges: B:H.75, B:H.146, B:H.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, S. et al., Structural Insights into the Catalytic Activity of Cyclobacterium marinum N -Acetylglucosamine Deacetylase. J.Agric.Food Chem. (2024)

Release Date

2024-01-03

Peptides

YdjC family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

YdjC family protein

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