MolNFT v1 · #152101 · protein
Crystal structure of dimeric wild type ficd complexed with ATP
6I7G · Adenosine monophosphate-protein transferase ficd: “Crystal structure of dimeric wild type ficd complexed with ATP”. X-ray diffraction, 1 ligand (ATP), 10 pockets (best druggability 0.62). MolNFT v1 #152101 on GenesisL1: 3D…
- PDB
- 6I7G
- Type
- protein
- Length
- 669 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.-, 3.1.4.-
- UniProt
- Q9BVA6
- Ligands
- ATP
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-, 3.1.4.-) | protein | 329 | 71% helix, 1% strand | Q9BVA6 |
| B | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-, 3.1.4.-) | protein | 340 | 71% helix, 1% strand | Q9BVA6 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.62 | 0.80 | 35 | empty |
| 2 | 241 | 0.61 | 0.81 | 27 | ATP |
| 3 | 244 | 0.58 | 0.79 | 27 | ATP |
| 4 | 183 | 0.56 | 0.79 | 28 | empty |
| 5 | 329 | 0.53 | 0.74 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6I7G · Crystal structure of dimeric wild type FICD complexed with ATP · 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 A 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 6I7G · PDBe 6I7G · UniProt Q9BVA6
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