SMTL ID : 3wl3.1

N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.44, D.47, H.155 Chain C: H.264 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.44, A:D.47, A:H.155 ZN.6: 4 residues within 4Å: Chain B: H.44, D.47, H.155 Ligands: PO4.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.44, B:D.47, B:D.47, B:H.155 ZN.11: 5 residues within 4Å: Chain B: H.264 Chain C: H.44, D.47, H.155 Ligands: PO4.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.44, C:D.47, C:H.155 ZN.13: 5 residues within 4Å: Chain D: H.44, D.47, H.155 Chain F: H.264 Ligands: PO4.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.44, D:D.47, D:H.155 ZN.18: 4 residues within 4Å: Chain E: H.44, D.47, H.155 Ligands: PO4.19 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.44, E:D.47, E:D.47, E:H.155 ZN.23: 5 residues within 4Å: Chain E: H.264 Chain F: H.44, D.47, H.155 Ligands: PO4.24 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.44, F:D.47, F:H.155

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: H.44, D.46, D.47, I.50, H.155 Chain C: H.264 Ligands: ZN.1, GOL.5 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Salt bridges: C:H.264, A:H.44, A:H.155 Hydrogen bonds: A:Y.196 PO4.3: 4 residues within 4Å: Chain A: R.157 Chain B: Y.120, R.157 Chain C: R.157 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Water bridges: B:R.157, B:R.157 Salt bridges: B:R.157, C:R.157, A:R.157 PO4.4: 6 residues within 4Å: Chain A: K.134, I.181 Chain D: K.134, I.181, L.183 Ligands: PO4.16 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Salt bridges: D:K.134, A:K.134 PO4.7: 8 residues within 4Å: Chain A: H.264 Chain B: H.44, D.46, D.47, I.50, H.155 Ligands: ZN.6, GOL.9 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.47 Water bridges: B:R.92, B:R.92 Salt bridges: B:H.44, B:H.155, A:H.264 PO4.8: 6 residues within 4Å: Chain B: K.134, I.181, L.183 Chain F: K.134, I.181, L.183 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Salt bridges: F:K.134, B:K.134 PO4.12: 7 residues within 4Å: Chain B: H.264 Chain C: H.44, D.46, D.47, I.50, H.155 Ligands: ZN.11 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Salt bridges: B:H.264, C:H.44, C:H.155 Hydrogen bonds: C:D.46 PO4.14: 8 residues within 4Å: Chain D: H.44, D.46, D.47, I.50, H.155 Chain F: H.264 Ligands: ZN.13, GOL.17 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Salt bridges: D:H.44, D:H.155, F:H.264 PO4.15: 4 residues within 4Å: Chain D: R.157 Chain E: Y.120, R.157 Chain F: R.157 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D, 1 interactions with chain F Water bridges: E:R.157, E:R.157 Salt bridges: E:R.157, D:R.157, F:R.157 PO4.16: 6 residues within 4Å: Chain A: K.134, I.181, L.183 Chain D: K.134, I.181 Ligands: PO4.4 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Salt bridges: D:K.134, A:K.134 PO4.19: 8 residues within 4Å: Chain D: H.264 Chain E: H.44, D.46, D.47, I.50, H.155 Ligands: ZN.18, GOL.21 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:D.47 Water bridges: E:R.92, E:R.92 Salt bridges: E:H.44, E:H.155, D:H.264 PO4.20: 6 residues within 4Å: Chain C: K.134, I.181, L.183 Chain E: K.134, I.181, L.183 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Salt bridges: E:K.134, C:K.134 PO4.24: 7 residues within 4Å: Chain E: H.264 Chain F: H.44, D.46, D.47, I.50, H.155 Ligands: ZN.23 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:D.46 Salt bridges: F:H.44, F:H.155, E:H.264

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: H.44, G.77, R.92, D.115, H.152, Q.223 Ligands: PO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.46, A:R.92, A:R.92, A:D.115, A:H.152 GOL.9: 8 residues within 4Å: Chain B: H.44, G.74, G.77, R.92, D.115, H.152, Q.223 Ligands: PO4.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.74, B:R.92, B:R.92, B:H.152 Water bridges: B:D.46, B:Q.223 GOL.10: 9 residues within 4Å: Chain A: R.122, K.126 Chain B: M.76, R.114, E.117 Chain D: L.111, N.112, Y.113, D.127 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:R.114, A:K.126, A:K.126, D:N.112 GOL.17: 7 residues within 4Å: Chain D: H.44, G.77, R.92, D.115, H.152, Q.223 Ligands: PO4.14 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.46, D:R.92, D:R.92, D:D.115, D:H.152 GOL.21: 8 residues within 4Å: Chain E: H.44, G.74, G.77, R.92, D.115, H.152, Q.223 Ligands: PO4.19 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.74, E:R.92, E:R.92, E:H.152 Water bridges: E:D.46, E:Q.223 GOL.22: 9 residues within 4Å: Chain A: L.111, N.112, Y.113, D.127 Chain D: R.122, K.126 Chain E: M.76, R.114, E.117 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: E:R.114, D:K.126, D:K.126, A:N.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mine, S. et al., Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase. Febs J. (2014)

Release Date

2014-05-07

Peptides

Putative uncharacterized protein PH0499: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Putative uncharacterized protein PH0499

Related Entries With Identical Sequence