MolNFT v1 · #171137 · protein
Capsule O-acetyltransferase of neisseria meningitidis serogroup a in complex with caged gadolinium
6YUO · Sacc: “Capsule O-acetyltransferase of neisseria meningitidis serogroup a in complex with caged gadolinium”. X-ray diffraction, 2 ligands (GD3, CL), 4 pockets (best druggability 0.47). MolNFT v1 #171137 on GenesisL1: 3D structure…
- PDB
- 6YUO
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sacc
- UniProt
- O68216
- Ligands
- GD3, CL
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sacc | protein | 241 | 43% helix, 23% strand | O68216 |
| B | Sacc | protein | 244 | 42% helix, 21% strand | O68216 |
Ligands and binding sites
- GD3 · Gadolinium ion · metal · 2 copies
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.47 | 0.75 | 34 | CL |
| 2 | 202 | 0.47 | 0.75 | 33 | empty |
| 3 | 160 | 0.45 | 0.75 | 30 | CL |
| 4 | 61 | 0.26 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 924 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6YUO · Capsule O-acetyltransferase of Neisseria meningitidis serogroup A in complex with caged… · 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 O68216
- Elsewhere: RCSB PDB 6YUO · PDBe 6YUO · UniProt O68216
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