Research workbench
Ancestral endocellulase Cel5A
Analyse Ancestral endocellulase Cel5A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GJF
- Type
- protein
- Length
- 1,818 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- synthetic construct
- Molecule
- Endoglucanase
- EC
- 3.2.1.4
- Ligands
- NA
- Pockets
- 17 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.45 · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Endoglucanase (EC 3.2.1.4) | protein | 303 | 41% helix, 19% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 10 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 11 copies · chains A, F, B, C, D, E
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.66 | 0.77 | 68 | empty |
| 2 | 319 | 0.65 | 0.80 | 43 | EDO, GOL |
| 3 | 321 | 0.64 | 0.80 | 43 | GOL |
| 4 | 405 | 0.64 | 0.78 | 45 | EDO, GOL |
| 5 | 401 | 0.62 | 0.77 | 42 | GOL |
Interfaces
7 interfaces between chains.
- B–E · 653 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 649 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 592 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 565 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 236 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6GJF · Ancestral endocellulase CEL5A · 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 6GJF · PDBe 6GJF
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