MolNFT v1 · #145947 · protein
Crystal structure of prevotella bryantii endo-beta-MANNANASE/ENDO- beta-glucanase PBGH26A-GH5A
6D2W · Aryl-phospho-beta-D-glucosidase bglc, GH1 family: “Crystal structure of prevotella bryantii endo-beta-MANNANASE/ENDO- beta-glucanase PBGH26A-GH5A”. X-ray diffraction, 11 pockets (best druggability 0.72). MolNFT v1 #145947 on…
- PDB
- 6D2W
- Type
- protein
- Length
- 1,372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aryl-phospho-beta-D-glucosidase bglc, GH1 family
- UniProt
- D8DY19
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aryl-phospho-beta-D-glucosidase bglc, GH1 family | protein | 687 | 40% helix, 14% strand | D8DY19 |
| B | Aryl-phospho-beta-D-glucosidase bglc, GH1 family | protein | 685 | 39% helix, 15% strand | D8DY19 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.72 | 0.83 | 47 | GOL |
| 2 | 385 | 0.70 | 0.82 | 45 | empty |
| 3 | 786 | 0.69 | 0.76 | 77 | empty |
| 4 | 339 | 0.67 | 0.81 | 49 | empty |
| 5 | 245 | 0.63 | 0.82 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 577 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6D2W · Crystal structure of Prevotella bryantii endo-beta-mannanase/endo-beta-glucanase… · 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 D8DY19
- Elsewhere: RCSB PDB 6D2W · PDBe 6D2W · UniProt D8DY19
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