Research workbench
The crystal structure of celk CBM4 from clostridium thermocellum
Analyse The crystal structure of celk CBM4 from clostridium thermocellum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P6B
- Type
- protein
- Length
- 372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulose 1,4-beta-cellobiosidase
- EC
- 3.2.1.91
- UniProt
- P0C2S1
- Ligands
- CA, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellulose 1,4-beta-cellobiosidase (EC 3.2.1.91) | protein | 186 | 5% helix, 48% strand | P0C2S1 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.70 | 0.83 | 39 | ACT |
| 2 | 93 | 0.38 | 0.76 | 20 | SO4, GOL |
| 3 | 81 | 0.36 | 0.76 | 18 | empty |
| 4 | 64 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 635 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3P6B · The crystal structure of CelK CBM4 from Clostridium thermocellum · the same entry in another collection · chain A against A, TM-score 1.00
- P0C2S1 · AlphaFold monomer V2.0 prediction for cellulose 1,4-beta- cellobiosidase (P0C2S1) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0C2S1
- Elsewhere: RCSB PDB 3P6B · PDBe 3P6B · UniProt P0C2S1
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