Research workbench
Structure of a family 84 glycoside hydrolase and a family 32 carbohydrate-binding module in tandem from clostridium perfringens.
Analyse Structure of a family 84 glycoside hydrolase and a family 32… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V5D
- Type
- protein
- Length
- 722 residues
- Chains
- 1
- 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
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glcnacase nagj (EC 3.2.1.52) | protein | 722 | 37% helix, 21% strand | Q0TR53 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.53 | 0.81 | 31 | empty |
| 2 | 58 | 0.48 | 0.85 | 16 | empty |
| 3 | 114 | 0.48 | 0.79 | 14 | empty |
| 4 | 100 | 0.46 | 0.80 | 16 | empty |
| 5 | 127 | 0.46 | 0.78 | 29 | empty |
Compared structures
- 2V5D · Structure of a Family 84 Glycoside Hydrolase and a Family 32 Carbohydrate-Binding Module… · 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 0.98
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 Q0TR53
- Elsewhere: RCSB PDB 2V5D · PDBe 2V5D · UniProt Q0TR53
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