Research workbench
Family 84 glycoside hydrolase from clostridium perfringens, 2.1 ångström structure
Analyse Family 84 glycoside hydrolase from clostridium perfringens, 2.1 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V5C
- Type
- protein
- Length
- 1,168 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase nagj
- EC
- 3.2.1.52
- UniProt
- Q0TR53
- Ligands
- CA, NA
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-glcnacase nagj (EC 3.2.1.52) | protein | 584 | 48% helix, 15% strand | Q0TR53 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CAC · Cacodylate ion · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.76 | 0.79 | 85 | CA, CAC |
| 2 | 404 | 0.69 | 0.81 | 56 | CAC |
| 3 | 370 | 0.69 | 0.82 | 55 | CAC |
| 4 | 170 | 0.50 | 0.78 | 31 | empty |
| 5 | 184 | 0.44 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1069 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2V5C · Family 84 glycoside hydrolase from Clostridium perfringens, 2.1 Angstrom structure · the same entry in another collection · chain A against A, TM-score 1.00
- Q0TR53 · AlphaFold monomer V2.0 prediction for O-glcnacase nagj (Q0TR53) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q0TR53
- Elsewhere: RCSB PDB 2V5C · PDBe 2V5C · UniProt Q0TR53
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