MolNFT v1 · #107113 · protein

ATP bound to eukaryotic fic domain containing protein

4U07 · Adenosine monophosphate-protein transferase ficd: “ATP bound to eukaryotic fic domain containing protein”. X-ray diffraction, 2 ligands (ATP, MG), 14 pockets (best druggability 0.60). MolNFT v1 #107113 on GenesisL1: 3D structure…

PDB: 4U07
Type: protein
Length: 646 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: ATP, MG
Pockets: 14 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 68% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-)	protein	323	68% helix, 1% strand	Q9BVA6

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · 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

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	214	0.60	0.81	27	MG, ATP
2	196	0.60	0.82	28	MG, ATP
3	159	0.58	0.82	24	empty
4	169	0.56	0.80	29	empty
5	61	0.36	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 853 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4U07 · ATP bound to eukaryotic FIC domain containing protein · 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 4U07 · PDBe 4U07 · UniProt Q9BVA6

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