Research workbench
Family 89 glycoside hydrolase from clostridium perfringens in complex with beta-N-acetyl-D-glucosamine
Analyse Family 89 glycoside hydrolase from clostridium perfringens in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VCA
- Type
- protein
- Length
- 886 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-N-acetylglucosaminidase
- EC
- 3.2.1.50
- UniProt
- Q0TST1
- Ligands
- NAG, CA, SO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-N-acetylglucosaminidase (EC 3.2.1.50) | protein | 886 | 41% helix, 17% strand | Q0TST1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.78 | 0.99 | 20 | GOL |
| 2 | 75 | 0.72 | 0.96 | 20 | empty |
| 3 | 270 | 0.69 | 0.84 | 28 | empty |
| 4 | 407 | 0.66 | 0.80 | 52 | empty |
| 5 | 109 | 0.65 | 0.88 | 21 | NAG, GOL |
Compared structures
- 2VCA · Family 89 glycoside hydrolase from Clostridium perfringens in complex with… · 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 Q0TST1
- Elsewhere: RCSB PDB 2VCA · PDBe 2VCA · UniProt Q0TST1
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