Research workbench

UBA1 in complex with ATP

Analyse UBA1 in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ZH9
Type: protein
Length: 1,005 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-activating enzyme E1 1
EC: 6.2.1.45
UniProt: P22515
Ligands: ATP, MG, K, SO4, CL
Pockets: 12 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45)	protein	1005	41% helix, 17% strand	P22515

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal · 3 copies · chains A
K · Potassium ion · metal · chains A
SO4 · Sulfate ion · ion · chains A
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 10 copies · chains A
ACT · Acetate ion · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	582	0.69	0.78	65	ATP, MG, GOL
2	589	0.63	0.75	52	empty
3	450	0.60	0.75	47	GOL, CL
4	346	0.58	0.76	45	empty
5	370	0.58	0.75	44	empty

Compared structures

7ZH9 · Uba1 in complex with ATP · the same entry in another collection · chain A against A, TM-score 1.00
P22515 · AlphaFold monomer V2.0 prediction for ubiquitin-activating enzyme E1 1 (P22515) · 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 P22515
Elsewhere: RCSB PDB 7ZH9 · PDBe 7ZH9 · UniProt P22515

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