MolNFT v1 · #51989 · protein
Family 51 carbohydrate binding module from a family 98 glycoside hydrolase produced by clostridium perfringens in complex with blood group B-trisaccharide ligand.
2VNO · CPE0329: “Family 51 carbohydrate binding module from a family 98 glycoside hydrolase produced by clostridium…”. X-ray diffraction, 3 ligands (GAL, FUC, CA), 1 pocket (best druggability 0.67). MolNFT v1 #51989 on GenesisL1: 3D…
- PDB
- 2VNO
- Type
- protein
- Length
- 344 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CPE0329
- EC
- 3.2.1.-
- UniProt
- Q8XNK4
- Ligands
- GAL, FUC, CA
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CPE0329 (EC 3.2.1.-) | protein | 171 | 5% helix, 43% strand | Q8XNK4 |
| B | CPE0329 (EC 3.2.1.-) | protein | 173 | 5% helix, 45% strand | Q8XNK4 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.67 | 0.80 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 510 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2VNO · Family 51 carbohydrate binding module from a family 98 glycoside hydrolase produced by… · 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 Q8XNK4
- Elsewhere: RCSB PDB 2VNO · PDBe 2VNO · UniProt Q8XNK4
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