Research workbench
A family 32 carbohydrate-binding module, from the mu toxin produced by clostridium perfringens, in complex with beta-D-glcnac-BETA(1,2) mannose
Analyse A family 32 carbohydrate-binding module, from the mu toxin produced by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WDB
- Type
- protein
- Length
- 569 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyaluronoglucosaminidase
- EC
- 3.2.1.35
- UniProt
- P26831
- Ligands
- MAN, NAG, CA
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronoglucosaminidase (EC 3.2.1.35) | protein | 139 | 6% helix, 55% strand | P26831 |
| B | Hyaluronoglucosaminidase (EC 3.2.1.35) | protein | 146 | 5% helix, 55% strand | P26831 |
| C | Hyaluronoglucosaminidase (EC 3.2.1.35) | protein | 141 | 6% helix, 54% strand | P26831 |
| D | Hyaluronoglucosaminidase (EC 3.2.1.35) | protein | 143 | 3% helix, 55% strand | P26831 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
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 | 780 | 0.79 | 0.83 | 87 | empty |
| 2 | 106 | 0.48 | 0.80 | 25 | empty |
| 3 | 63 | 0.45 | 0.83 | 18 | empty |
| 4 | 98 | 0.36 | 0.75 | 30 | empty |
Interfaces
6 interfaces between chains.
- B–D · 690 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 424 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 375 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 352 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 178 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2WDB · A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium… · the same entry in another collection · chain D against D, TM-score 1.00
- P26831 · AlphaFold monomer V2.0 prediction for hyaluronoglucosaminidase (P26831) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P26831
- Elsewhere: RCSB PDB 2WDB · PDBe 2WDB · UniProt P26831
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.