SMTL ID : 4xm1.1

N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus in the presence of cadmium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

8 x CD: CADMIUM ION(Non-covalent)

CD.1: 5 residues within 4Å: Chain A: H.40, D.43, H.151 Chain C: H.259 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.40, A:D.43, A:D.43, A:H.151 CD.2: 5 residues within 4Å: Chain A: E.225 Chain C: M.1 Ligands: CL.4, CL.10, CL.11 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.225, A:E.225 CD.6: 3 residues within 4Å: Chain B: H.40, D.43, H.151 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.40, B:D.43, B:H.151, H2O.5, H2O.5 CD.8: 3 residues within 4Å: Chain C: H.40, D.43, H.151 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.40, C:D.43, C:D.43, H2O.5, H2O.5 CD.12: 5 residues within 4Å: Chain D: H.40, D.43, H.151 Chain F: H.259 Ligands: GOL.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.40, D:D.43, D:D.43, D:H.151, H2O.14 CD.13: 5 residues within 4Å: Chain D: E.225 Chain F: M.1 Ligands: CL.15, CL.21, CL.22 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.225, D:E.225 CD.17: 3 residues within 4Å: Chain E: H.40, D.43, H.151 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.40, E:D.43, E:D.43, E:H.151, H2O.12 CD.19: 4 residues within 4Å: Chain E: H.259 Chain F: H.40, D.43, H.151 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.40, F:D.43, F:D.43, F:H.151, H2O.12

6 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.3: 6 residues within 4Å: Chain A: Y.116, F.156 Chain B: R.152, F.156 Ligands: HEZ.7, HEZ.9 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.156, A:F.156 Water bridges: A:R.153, B:P.141 HEZ.7: 6 residues within 4Å: Chain B: F.156 Chain C: P.141, W.142, R.152 Ligands: HEZ.3, HEZ.9 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:R.152 Hydrophobic interactions: B:F.156 HEZ.9: 6 residues within 4Å: Chain A: P.141, R.152 Chain C: Y.116, F.156 Ligands: HEZ.3, HEZ.7 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.156, C:F.156 Water bridges: C:W.142, C:R.153, A:P.141, A:W.142, A:L.143 HEZ.14: 5 residues within 4Å: Chain D: P.141, R.152 Chain F: F.156 Ligands: HEZ.18, HEZ.20 3 PLIP interactions: 3 interactions with chain D Water bridges: D:P.141, D:W.142, D:R.152 HEZ.18: 5 residues within 4Å: Chain D: F.156 Chain E: P.141, R.152 Ligands: HEZ.14, HEZ.20 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:F.156, D:F.156 Water bridges: E:R.152 HEZ.20: 5 residues within 4Å: Chain E: F.156 Chain F: P.141, R.152 Ligands: HEZ.14, HEZ.18 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:P.141 Water bridges: F:R.152 Hydrophobic interactions: E:F.156

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

CL.4: 3 residues within 4Å: Chain A: E.225 Ligands: CD.2, CL.11 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: E.225 Chain C: M.1 Ligands: CD.2, CL.11 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: E.225 Chain C: M.1 Ligands: CD.2, CL.4, CL.10 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain D: E.225 Ligands: CD.13, CL.21, CL.22 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain D: E.225 Chain F: M.1 Ligands: CD.13, CL.15, CL.22 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain F: M.1 Ligands: CD.13, CL.15, CL.21 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: H.40, D.42, D.43, I.46, H.151 Chain C: H.259, I.260 Ligands: CD.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.42, A:R.88, C:H.259 GOL.16: 9 residues within 4Å: Chain D: H.40, D.42, D.43, I.46, R.88, H.151 Chain F: H.259, I.260 Ligands: CD.12 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:D.43, D:R.88, F:H.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, T. et al., Multiple crystal forms of N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus. Acta Crystallogr.,Sect.F (2015)

Release Date

2015-06-10

Peptides

Uncharacterized protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Uncharacterized protein

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