MolNFT v1 · #121514 · protein
The crystal structure of thermostable xylanase mutant
5HXV · Endo-1,4-beta-xylanase: “The crystal structure of thermostable xylanase mutant”. X-ray diffraction, 17 pockets (best druggability 0.83). MolNFT v1 #121514 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HXV
- Type
- protein
- Length
- 2,268 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- W8VR85
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 189 | 5% helix, 65% strand | W8VR85 |
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.83 | 0.85 | 112 | empty |
| 2 | 988 | 0.83 | 0.84 | 98 | empty |
| 3 | 922 | 0.81 | 0.83 | 105 | empty |
| 4 | 1152 | 0.81 | 0.82 | 114 | empty |
| 5 | 1000 | 0.77 | 0.79 | 102 | empty |
Interfaces
21 interfaces between chains.
- C–J · 627 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 506 Ų buried · 8 hydrogen bonds · protein-protein
- D–I · 479 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 457 Ų buried · 7 hydrogen bonds · protein-protein
- H–J · 450 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5HXV · The crystal structure of thermostable xylanase mutant · 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 W8VR85
- Elsewhere: RCSB PDB 5HXV · PDBe 5HXV · UniProt W8VR85
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