Research workbench
Unique ligand binding specificity for a family 32 carbohydrate- binding module from the mu toxin produced by clostridium perfringens
Analyse Unique ligand binding specificity for a family 32 carbohydrate- binding module… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W1Q
- Type
- protein
- Length
- 279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyaluronoglucosaminidase
- EC
- 3.2.1.35
- UniProt
- P26831
- Ligands
- CA, NA
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronoglucosaminidase (EC 3.2.1.35) | protein | 140 | 6% helix, 55% strand | P26831 |
| B | Hyaluronoglucosaminidase (EC 3.2.1.35) | protein | 139 | 6% helix, 55% strand | P26831 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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 | 292 | 0.55 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 243 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2W1Q · Unique ligand binding specificity for a family 32 Carbohydrate- Binding Module from the… · the same entry in another collection · chain A against A, TM-score 1.00
- P26831 · AlphaFold monomer V2.0 prediction for hyaluronoglucosaminidase (P26831) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 2W1Q · PDBe 2W1Q · UniProt P26831
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