Research workbench

UBA1 in complex with ub-MLN4924 covalent adduct

Analyse UBA1 in complex with ub-MLN4924 covalent adduct in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5L6I
Type: protein
Length: 2,236 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-activating enzyme E1 1; Ubiquitin-40S ribosomal protein S31
EC: 6.2.1.45
UniProt: P22515, P05759
Ligands: B39, CL, SO4
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45)	protein	1007	42% helix, 17% strand	P22515
B, D	Ubiquitin-40S ribosomal protein S31	protein	76	24% helix, 33% strand	P05759
C	Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45)	protein	1004	42% helix, 17% strand	P22515
E	Ubiquitin-40S ribosomal protein S31	protein	73	25% helix, 33% strand	P05759

Ligands and binding sites

B39 · [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate · ligand · 2 copies · chains A, B, C, D
CL · Chloride ion · ion · 16 copies · chains A, B, C, D, E
SO4 · Sulfate ion · ion · 2 copies · chains A, C
GOL · Glycerol · additive · 16 copies · chains A, C

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	705	0.76	0.81	72	empty
2	572	0.75	0.82	90	CL, GOL
3	412	0.73	0.83	64	empty
4	352	0.65	0.80	47	SO4, B39
5	329	0.64	0.80	42	SO4, B39

Interfaces

5 interfaces between chains.

A–C · 1982 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1641 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 1624 Å² buried · 31 hydrogen bonds · protein-protein
C–E · 788 Å² buried · 3 hydrogen bonds · protein-protein
D–E · 23 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (covalent ligand, oxidation).

Compared structures

5L6I · Uba1 in complex with Ub-MLN4924 covalent adduct · the same entry in another collection · chain B against B, 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 0.99

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
Every structure of UniProt P05759
Elsewhere: RCSB PDB 5L6I · PDBe 5L6I · UniProt P22515 · UniProt P05759

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.