Research workbench
The structure of the beta-3-deoxy-D-manno-oct-2-ulosonic acid transferase domain from wbbb
Analyse The structure of the beta-3-deoxy-D-manno-oct-2-ulosonic acid transferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FA0
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative N-acetyl glucosaminyl transferase
- UniProt
- Q6U8B0
- Ligands
- CL
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative N-acetyl glucosaminyl transferase | protein | 394 | 45% helix, 14% strand | Q6U8B0 |
| B | Putative N-acetyl glucosaminyl transferase | protein | 388 | 43% helix, 14% strand | Q6U8B0 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
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 | 870 | 0.75 | 0.79 | 74 | empty |
| 2 | 461 | 0.74 | 0.83 | 31 | CL |
| 3 | 824 | 0.73 | 0.78 | 72 | empty |
| 4 | 85 | 0.35 | 0.75 | 14 | empty |
| 5 | 77 | 0.34 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1484 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 5FA0 · The structure of the beta-3-deoxy-D-manno-oct-2-ulosonic acid transferase domain from WbbB · 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 Q6U8B0
- Elsewhere: RCSB PDB 5FA0 · PDBe 5FA0 · UniProt Q6U8B0
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