Research workbench
The clostridium cellulolyticum dockerin displays a dual binding mode for its cohesin partner
Analyse The clostridium cellulolyticum dockerin displays a dual binding mode for its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VN5
- Type
- protein
- Length
- 401 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scaffolding protein; Endoglucanase a
- UniProt
- Q45996, P17901
- Ligands
- CA
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scaffolding protein | protein | 142 | 5% helix, 56% strand | Q45996 |
| B | Endoglucanase a | protein | 56 | 50% helix, 0% strand | P17901 |
| C | Scaffolding protein | protein | 148 | 5% helix, 53% strand | Q45996 |
| D | Endoglucanase a | protein | 55 | 47% helix, 0% strand | P17901 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.28 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 787 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 709 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 222 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2VN5 · The Clostridium cellulolyticum dockerin displays a dual binding mode for its cohesin… · the same entry in another collection · chain A against A, TM-score 1.00
- P17901 · AlphaFold monomer V2.0 prediction for endoglucanase a (P17901) · a predicted model of the same protein · chain D 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 Q45996
- Every structure of UniProt P17901
- Elsewhere: RCSB PDB 2VN5 · PDBe 2VN5 · UniProt Q45996 · UniProt P17901
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