MolNFT v1 · #110084 · protein
N,N'-diacetylchitobiose deacetylase (semet derivative) from pyrococcus furiosus in the presence of cadmium
4XLZ · Uncharacterized protein: “N,N'-diacetylchitobiose deacetylase (semet derivative) from pyrococcus furiosus in the presence of cadmium”. X-ray diffraction, 2 ligands (CD, CL), 20 pockets (best druggability 0.82). MolNFT v1 #110084 on…
- PDB
- 4XLZ
- Type
- protein
- Length
- 1,602 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 · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uncharacterized protein | protein | 267 | 45% helix, 15% strand | Q8U3V1 |
Ligands and binding sites
- CD · Cadmium ion · metal · 18 copies · chains A, C, B, D, F, E
- CL · Chloride ion · ion · 24 copies · chains A, B, C, D, E, F
- HEZ · Hexane-1,6-diol · additive · 45 copies · chains A, C, E, B, D, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 8 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.82 | 0.84 | 48 | HEZ, TRS, CL |
| 2 | 991 | 0.81 | 0.82 | 49 | HEZ, TRS, CL |
| 3 | 812 | 0.77 | 0.80 | 56 | HEZ, CD, TRS |
| 4 | 710 | 0.77 | 0.81 | 57 | HEZ, TRS |
| 5 | 783 | 0.76 | 0.81 | 61 | HEZ, CD, TRS |
Interfaces
12 interfaces between chains.
- D–F · 1902 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1897 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1890 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1889 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1881 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified, 1 covalent (engineered, additive adduct).
Compared structures
- 4XLZ · N,N'-diacetylchitobiose deacetylase (SeMet derivative) from Pyrococcus furiosus in the… · the same entry in another collection · chain B against B, 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 4XLZ · PDBe 4XLZ · UniProt Q8U3V1
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