MolNFT v1 · #108815 · protein
Crystal structure of C-terminal domain of putative chitinase from desulfitobacterium hafniense dcb-2
4WIW · Glycoside hydrolase family 18: “Crystal structure of C-terminal domain of putative chitinase from desulfitobacterium hafniense dcb-2”. X-ray diffraction, 2 ligands (CA, CL), 20 pockets (best druggability 0.68). MolNFT v1 #108815 on…
- PDB
- 4WIW
- Type
- protein
- Length
- 2,089 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 18
- UniProt
- B8FWJ2
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Glycoside hydrolase family 18 | protein | 348 | 37% helix, 24% strand | B8FWJ2 |
| D | Glycoside hydrolase family 18 | protein | 349 | 38% helix, 24% strand | B8FWJ2 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 2 copies · chains A, F
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.68 | 0.78 | 67 | empty |
| 2 | 158 | 0.48 | 0.77 | 31 | empty |
| 3 | 218 | 0.48 | 0.74 | 29 | empty |
| 4 | 176 | 0.47 | 0.75 | 29 | empty |
| 5 | 199 | 0.46 | 0.74 | 27 | empty |
Interfaces
7 interfaces between chains.
- B–F · 792 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 768 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 741 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 209 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 54 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 66 modified (engineered).
Compared structures
- 4WIW · Crystal structure of C-terminal domain of putative chitinase from Desulfitobacterium… · 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 B8FWJ2
- Elsewhere: RCSB PDB 4WIW · PDBe 4WIW · UniProt B8FWJ2
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