MolNFT v1 · #171139 · protein
Capsule O-acetyltransferase of neisseria meningitidis serogroup a in complex with polysaccharide
6YUQ: “Capsule O-acetyltransferase of neisseria meningitidis serogroup a in complex with polysaccharide”. X-ray diffraction, 3 ligands (BMX, BM3, CL), 4 pockets (best druggability 0.51). MolNFT v1 #171139 on GenesisL1: 3D structure…
- PDB
- 6YUQ
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sacc
- UniProt
- O68216
- Ligands
- BMX, BM3, CL
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sacc | protein | 245 | 41% helix, 22% strand | O68216 |
Ligands and binding sites
- BMX · 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose · ligand · 3 copies · chains A
- BM3 · 2-acetamido-2-deoxy-alpha-D-mannopyranose · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PGE · Triethylene glycol · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.51 | 0.76 | 36 | EDO |
| 2 | 157 | 0.45 | 0.76 | 33 | CL |
| 3 | 103 | 0.38 | 0.76 | 22 | CL, BMX |
| 4 | 57 | 0.26 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 912 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6YUQ · Capsule O-acetyltransferase of Neisseria meningitidis serogroup A 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 O68216
- Elsewhere: RCSB PDB 6YUQ · PDBe 6YUQ · UniProt O68216
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