MolNFT v1 · #163315 · protein
Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium PG7
6RZD: “Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium PG7”. X-ray diffraction, 2 ligands (TAM, SO4), 5 pockets (best druggability 0.85). MolNFT v1 #163315 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6RZD
- Type
- protein
- Length
- 992 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosialidase from uncultured bacterium PG7
- EC
- 3.2.1.18
- Ligands
- TAM, SO4
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exosialidase from uncultured bacterium PG7 (EC 3.2.1.18) | protein | 496 | 30% helix, 22% strand | — |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.85 | 0.86 | 102 | GOL, ACT |
| 2 | 380 | 0.67 | 0.80 | 39 | empty |
| 3 | 396 | 0.66 | 0.79 | 36 | empty |
| 4 | 157 | 0.55 | 0.80 | 27 | TAM, SO4, GOL |
| 5 | 138 | 0.53 | 0.80 | 26 | SO4, TAM, GOL |
Interfaces
1 interface between chains.
- A–B · 1819 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6RZD · Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 · 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
- Elsewhere: RCSB PDB 6RZD · PDBe 6RZD
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