Research workbench
Chargeless variant of the cellulose-binding domain from cellulomonas fimi
Analyse Chargeless variant of the cellulose-binding domain from cellulomonas fimi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QFS
- Type
- protein
- Length
- 841 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EXOGLUCANASE/XYLANASE
- EC
- 3.2.1.91, 3.2.1.8
- UniProt
- P07986
- Ligands
- 1PS, ETE
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | EXOGLUCANASE/XYLANASE (EC 3.2.1.91, 3.2.1.8) | protein | 104 | 0% helix, 59% strand | P07986 |
| B, D, G, H | EXOGLUCANASE/XYLANASE (EC 3.2.1.91, 3.2.1.8) | protein | 106 | 0% helix, 59% strand | P07986 |
| F | EXOGLUCANASE/XYLANASE (EC 3.2.1.91, 3.2.1.8) | protein | 105 | 0% helix, 58% strand | P07986 |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 4 copies · chains B, C, D, A, E, G, F, H
- ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · 2 copies · chains D, A, E
- FMT · Formic acid · additive · 25 copies · chains A, E, B, C, F, D, G, H
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B, C, F, G, D, E
- ACT · Acetate ion · additive · 8 copies · chains A, C, D, G, H
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains D, H
- GOL · Glycerol · additive · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.70 | 0.74 | 109 | FMT, EDO, 1PS |
| 2 | 960 | 0.69 | 0.74 | 101 | FMT, 1PS, EDO, ETE |
| 3 | 115 | 0.43 | 0.77 | 24 | FMT, GOL |
| 4 | 77 | 0.43 | 0.80 | 22 | FMT |
| 5 | 120 | 0.42 | 0.77 | 29 | ACT |
Interfaces
17 interfaces between chains.
- D–E · 440 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 432 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 411 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 402 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 379 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6QFS · Chargeless variant of the Cellulose-binding domain from Cellulomonas fimi · the same entry in another collection · chain H against H, TM-score 1.00
- P07986 · AlphaFold monomer V2.0 prediction for EXOGLUCANASE/XYLANASE (P07986) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P07986
- Elsewhere: RCSB PDB 6QFS · PDBe 6QFS · UniProt P07986
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