MolNFT v1 · #107538 · protein
ATBBE15
4UD8 · FAD-binding and bbe domain-containing protein: “ATBBE15”. X-ray diffraction, 4 ligands (FAD, NAG, NA), 5 pockets (best druggability 0.84). MolNFT v1 #107538 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UD8
- Type
- protein
- Length
- 997 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-binding and bbe domain-containing protein
- UniProt
- O64743
- Ligands
- FAD, NAG, NA, K
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-binding and bbe domain-containing protein | protein | 500 | 38% helix, 22% strand | O64743 |
| B | FAD-binding and bbe domain-containing protein | protein | 497 | 37% helix, 22% strand | O64743 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- K · Potassium ion · metal · chains B
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.84 | 0.89 | 68 | FAD, PE5 |
| 2 | 614 | 0.83 | 0.88 | 67 | FAD, PE5 |
| 3 | 1057 | 0.78 | 0.80 | 87 | empty |
| 4 | 81 | 0.34 | 0.75 | 17 | empty |
| 5 | 73 | 0.28 | 0.72 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 365 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 glycan, 1 disulfide (flavinylation, N-glycosylation, disulfide).
Compared structures
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 O64743
- Elsewhere: RCSB PDB 4UD8 · PDBe 4UD8 · UniProt O64743
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