Research workbench
N,N'-diacetylchitobiose deacetylase (semet derivative) from pyrococcus furiosus in the absence of cadmium
Analyse N,N'-diacetylchitobiose deacetylase (semet derivative) from pyrococcus furiosus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XM0
- Type
- protein
- Length
- 1,569 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q8U3V1
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Uncharacterized protein | protein | 264 | 43% helix, 16% strand | Q8U3V1 |
| B | Uncharacterized protein | protein | 255 | 38% helix, 17% strand | Q8U3V1 |
| C, D, E | Uncharacterized protein | protein | 262 | 41% helix, 16% strand | Q8U3V1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.82 | 0.84 | 46 | empty |
| 2 | 779 | 0.82 | 0.85 | 40 | empty |
| 3 | 797 | 0.77 | 0.81 | 55 | ZN |
| 4 | 763 | 0.77 | 0.81 | 59 | empty |
| 5 | 720 | 0.76 | 0.81 | 56 | ZN |
Interfaces
12 interfaces between chains.
- D–F · 1774 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1717 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1709 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1698 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1620 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 4XM0 · N,N'-diacetylchitobiose deacetylase (SeMet derivative) from Pyrococcus furiosus in the… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8U3V1
- Elsewhere: RCSB PDB 4XM0 · PDBe 4XM0 · UniProt Q8U3V1
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