MolNFT v1 · #163351 · protein
Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium PG7 in complex with 3-deoxy-D-glycero-D-galacto- 2-nonulosonic acid
6S0F: “Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium PG7 in complex with…”. X-ray diffraction, 2 ligands (KDN, SCN), 5 pockets (best druggability 0.86). MolNFT v1 #163351 on GenesisL1: 3D structure…
- PDB
- 6S0F
- Type
- protein
- Length
- 993 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
- KDN, SCN
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosialidase from uncultured bacterium PG7 (EC 3.2.1.18) | protein | 497 | 31% helix, 22% strand | — |
| B | Exosialidase from uncultured bacterium PG7 (EC 3.2.1.18) | protein | 496 | 30% helix, 23% strand | — |
Ligands and binding sites
- KDN · deamino-beta-neuraminic acid · sugar · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains B
- TRS · 2-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
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 | 1036 | 0.86 | 0.87 | 109 | GOL |
| 2 | 521 | 0.69 | 0.78 | 49 | GOL |
| 3 | 475 | 0.66 | 0.78 | 42 | empty |
| 4 | 274 | 0.58 | 0.78 | 35 | GOL, KDN |
| 5 | 230 | 0.55 | 0.77 | 34 | ACT, KDN |
Interfaces
1 interface between chains.
- A–B · 1795 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6S0F · 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 6S0F · PDBe 6S0F
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