Research workbench
N,N'-diacetylchitobiose deacetylase from pyrococcus furiosus in the presence of cadmium
Analyse N,N'-diacetylchitobiose deacetylase from pyrococcus furiosus in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XM1
- Type
- protein
- Length
- 1,575 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q8U3V1
- Ligands
- CD, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 263 | 46% helix, 15% strand | Q8U3V1 |
| B | Uncharacterized protein | protein | 261 | 45% helix, 15% strand | Q8U3V1 |
| C, F | Uncharacterized protein | protein | 267 | 43% helix, 15% strand | Q8U3V1 |
| D | Uncharacterized protein | protein | 260 | 47% helix, 15% strand | Q8U3V1 |
| E | Uncharacterized protein | protein | 257 | 44% helix, 15% strand | Q8U3V1 |
Ligands and binding sites
- CD · Cadmium ion · metal · 8 copies · chains A, C, B, D, F, E
- CL · Chloride ion · ion · 6 copies · chains A, C, D, F
- HEZ · Hexane-1,6-diol · additive · 6 copies · chains A, B, C, D, F, E
- GOL · Glycerol · additive · 2 copies · chains A, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.82 | 0.85 | 47 | HEZ |
| 2 | 852 | 0.82 | 0.84 | 45 | HEZ |
| 3 | 713 | 0.77 | 0.81 | 58 | CD |
| 4 | 747 | 0.76 | 0.81 | 55 | CD |
| 5 | 726 | 0.76 | 0.81 | 55 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1896 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1896 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1695 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1654 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1628 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4XM1 · N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus in the presence of cadmium · the same entry in another collection · chain D against D, 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 4XM1 · PDBe 4XM1 · UniProt Q8U3V1
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