SMTL ID : 8bgn.1

N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.40, D.43, H.151 Chain B: H.259 Ligands: EDO.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.40, A:D.43, A:H.151, H2O.1 ZN.5: 4 residues within 4Å: Chain B: H.40, D.43, H.151 Chain C: H.259 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.40, B:D.43, B:H.151, H2O.3 ZN.7: 4 residues within 4Å: Chain A: H.259 Chain C: H.40, D.43, H.151 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.40, C:D.43, C:D.43, C:H.151 ZN.10: 5 residues within 4Å: Chain D: H.40, D.43, H.151 Chain E: H.259 Ligands: EDO.11 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.40, D:D.43, D:H.151, H2O.5 ZN.14: 4 residues within 4Å: Chain E: H.40, D.43, H.151 Chain F: H.259 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.40, E:D.43, E:H.151, H2O.6 ZN.16: 4 residues within 4Å: Chain D: H.259 Chain F: H.40, D.43, H.151 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.40, F:D.43, F:D.43, F:H.151

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

EDO.2: 5 residues within 4Å: Chain A: H.40, G.73, R.88, D.111 Ligands: ZN.1 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:H.259, A:D.42 Hydrogen bonds: A:R.88, A:R.88, A:D.111 EDO.6: 4 residues within 4Å: Chain B: R.152 Chain C: Y.116 Ligands: EDO.8, EDO.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.152 Water bridges: B:P.141 EDO.8: 5 residues within 4Å: Chain B: P.149, R.152, F.156 Chain C: Y.116 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.149, B:R.152 EDO.9: 5 residues within 4Å: Chain A: Y.116 Chain C: P.149, R.152, A.153 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain D: H.40, G.73, R.88, D.111 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.88, D:R.88, D:D.111 Water bridges: D:D.42, E:H.259 EDO.15: 4 residues within 4Å: Chain E: R.152 Chain F: Y.116 Ligands: EDO.17, EDO.18 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.152 Water bridges: E:P.141 EDO.17: 5 residues within 4Å: Chain E: P.149, R.152, F.156 Chain F: Y.116 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:P.149, E:R.152 EDO.18: 5 residues within 4Å: Chain D: Y.116 Chain F: P.149, R.152, A.153 Ligands: EDO.15 No protein-ligand interaction detected (PLIP)

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

CL.3: 2 residues within 4Å: Chain A: R.54, D.200 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: K.122 Chain E: L.107, D.123 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain D: R.54, D.200 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: L.107, D.123 Chain D: K.122 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biniek-Antosiak, K. et al., Structural, Thermodynamic and Enzymatic Characterization of N , N -Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus. Int J Mol Sci (2022)

Release Date

2023-01-11

Peptides

Diacetylchitobiose deacetylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Diacetylchitobiose deacetylase

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