Research workbench
Structure of eukaryotic fic domain containing protein with ADP
Analyse Structure of eukaryotic fic domain containing protein with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U0S
- Type
- protein
- Length
- 647 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine monophosphate-protein transferase ficd
- EC
- 2.7.7.-
- UniProt
- Q9BVA6
- Ligands
- ADP, MG
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-) | protein | 323 | 71% helix, 1% strand | Q9BVA6 |
| B | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-) | protein | 324 | 70% helix, 2% strand | Q9BVA6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.61 | 0.82 | 29 | ADP, MG |
| 2 | 207 | 0.61 | 0.82 | 26 | ADP, MG |
| 3 | 177 | 0.61 | 0.83 | 26 | empty |
| 4 | 163 | 0.59 | 0.83 | 26 | empty |
| 5 | 179 | 0.47 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 828 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4U0S · Structure of Eukaryotic fic domain containing protein with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BVA6 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase ficd (Q9BVA6) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9BVA6
- Elsewhere: RCSB PDB 4U0S · PDBe 4U0S · UniProt Q9BVA6
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