MolNFT v1 · #118702 · protein
The structure of the beta-3-deoxy-D-manno-oct-2-ulosonic acid transferase domain of wbbb
5FA1 · Putative N-acetyl glucosaminyl transferase: “The structure of the beta-3-deoxy-D-manno-oct-2-ulosonic acid transferase domain of wbbb”. X-ray diffraction, 1 ligand (C5P), 8 pockets (best druggability 0.74). MolNFT v1 #118702 on…
- PDB
- 5FA1
- Type
- protein
- Length
- 780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative N-acetyl glucosaminyl transferase
- UniProt
- Q6U8B0
- Ligands
- C5P
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative N-acetyl glucosaminyl transferase | protein | 390 | 47% helix, 13% strand | Q6U8B0 |
| B | Putative N-acetyl glucosaminyl transferase | protein | 390 | 45% helix, 14% strand | Q6U8B0 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.74 | 0.79 | 68 | C5P |
| 2 | 686 | 0.74 | 0.80 | 64 | C5P |
| 3 | 598 | 0.69 | 0.78 | 60 | empty |
| 4 | 292 | 0.68 | 0.83 | 46 | empty |
| 5 | 192 | 0.64 | 0.85 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1114 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5FA1 · The structure of the beta-3-deoxy-D-manno-oct-2-ulosonic acid transferase domain of 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 5FA1 · PDBe 5FA1 · UniProt Q6U8B0
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