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Crystal structure of endoglucanase celq from clostridium thermocellum complexed with cellobiose and tris
Analyse Crystal structure of endoglucanase celq from clostridium thermocellum complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GXY
- Type
- protein
- Length
- 1,198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucanase
- EC
- 3.2.1.-
- UniProt
- Q9AJF8
- Ligands
- BGC, CA, CL, BR
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucanase (EC 3.2.1.-) | protein | 599 | 39% helix, 16% strand | Q9AJF8 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
- BR · Bromide ion · ion · 6 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.63 | 0.80 | 30 | empty |
| 2 | 239 | 0.54 | 0.77 | 32 | BGC, TRS |
| 3 | 235 | 0.53 | 0.76 | 34 | BGC, TRS |
| 4 | 59 | 0.31 | 0.76 | 18 | CL |
Interfaces
1 interface between chains.
- A–B · 694 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5GXY · Crystal structure of endoglucanase CelQ from Clostridium thermocellum complexed with… · 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 Q9AJF8
- Elsewhere: RCSB PDB 5GXY · PDBe 5GXY · UniProt Q9AJF8
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