MolNFT v1 · #168779 · protein
GH5-4 broad specificity endoglucanase from ruminococcus champanellensis with bound cellotriose
6WQV: “GH5-4 broad specificity endoglucanase from ruminococcus champanellensis with bound cellotriose”. X-ray diffraction, 3 ligands (BGC, GLC, NO3), 13 pockets (best druggability 0.71). MolNFT v1 #168779 on GenesisL1: 3D structure…
- PDB
- 6WQV
- Type
- protein
- Length
- 1,382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase
- UniProt
- D4LAX7
- Ligands
- BGC, GLC, NO3
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoglucanase | protein | 348 | 40% helix, 13% strand | D4LAX7 |
| B | Endoglucanase | protein | 346 | 40% helix, 13% strand | D4LAX7 |
| C, D | Endoglucanase | protein | 344 | 41% helix, 13% strand | D4LAX7 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 3 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.71 | 0.77 | 92 | NO3 |
| 2 | 385 | 0.60 | 0.76 | 45 | empty |
| 3 | 360 | 0.57 | 0.75 | 39 | empty |
| 4 | 353 | 0.56 | 0.75 | 37 | GLC, BGC |
| 5 | 319 | 0.55 | 0.75 | 41 | GLC, BGC |
Interfaces
5 interfaces between chains.
- C–D · 327 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 184 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 177 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 171 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WQV · GH5-4 broad specificity endoglucanase from Ruminococcus champanellensis with bound… · 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 D4LAX7
- Elsewhere: RCSB PDB 6WQV · PDBe 6WQV · UniProt D4LAX7
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