MolNFT v1 · #162817 · protein
Complex structure of virulence factor sgha mutant with its substrate sag
6RK2 · Beta-glucosidase: “Complex structure of virulence factor sgha mutant with its substrate sag”. X-ray diffraction, 1 ligand (6GR), 7 pockets (best druggability 0.76). MolNFT v1 #162817 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6RK2
- Type
- protein
- Length
- 905 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- A0A2I4PGZ0
- Ligands
- 6GR
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase (EC 3.2.1.21) | protein | 454 | 45% helix, 16% strand | A0A2I4PGZ0 |
| B | Beta-glucosidase (EC 3.2.1.21) | protein | 451 | 44% helix, 16% strand | A0A2I4PGZ0 |
Ligands and binding sites
- 6GR · 2-(alpha-L-altropyranosyloxy)benzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.76 | 0.90 | 33 | empty |
| 2 | 522 | 0.71 | 0.80 | 51 | 6GR |
| 3 | 485 | 0.70 | 0.80 | 49 | 6GR |
| 4 | 83 | 0.40 | 0.78 | 16 | empty |
| 5 | 72 | 0.36 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1033 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6RK2 · Complex structure of virulence factor SghA mutant with its substrate SAG · 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 A0A2I4PGZ0
- Elsewhere: RCSB PDB 6RK2 · PDBe 6RK2 · UniProt A0A2I4PGZ0
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