Research workbench
Crystal structure of a bacterial ig-like domain containing GH10 xylanase from termite gut
Analyse Crystal structure of a bacterial ig-like domain containing GH10 xylanase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HU8
- Type
- protein
- Length
- 3,614 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH10 xylanase
- EC
- 3.2.1.8
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GH10 xylanase (EC 3.2.1.8) | protein | 450 | 39% helix, 24% strand | — |
| B, C, D, E, F, G, H | GH10 xylanase (EC 3.2.1.8) | protein | 452 | 37% helix, 24% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F, H, G
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.81 | 0.82 | 132 | GOL |
| 2 | 1015 | 0.80 | 0.81 | 120 | SO4, GOL |
| 3 | 716 | 0.76 | 0.81 | 90 | GOL |
| 4 | 1149 | 0.75 | 0.78 | 98 | empty |
| 5 | 569 | 0.73 | 0.81 | 77 | SO4, GOL |
Interfaces
10 interfaces between chains.
- C–D · 970 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 951 Ų buried · 22 hydrogen bonds · protein-protein
- F–H · 943 Ų buried · 23 hydrogen bonds · protein-protein
- E–G · 840 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 559 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4HU8 · Crystal Structure of a Bacterial Ig-like Domain Containing GH10 Xylanase from Termite Gut · 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
- Elsewhere: RCSB PDB 4HU8 · PDBe 4HU8
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