MolNFT v1 · #185436 · protein

Crystal structure of human UBA6 in complex with ATP

7PVN · Ubiquitin-like modifier-activating enzyme 6: “Crystal structure of human UBA6 in complex with ATP”. X-ray diffraction, 4 ligands (ATP, CA, MG), 20 pockets (best druggability 0.76). MolNFT v1 #185436 on GenesisL1: 3D structure…

PDB: 7PVN
Type: protein
Length: 1,988 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-like modifier-activating enzyme 6
EC: 6.2.1.45
UniProt: A0AVT1
Ligands: ATP, CA, MG, CL
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-like modifier-activating enzyme 6 (EC 6.2.1.45)	protein	998	42% helix, 16% strand	A0AVT1
B	Ubiquitin-like modifier-activating enzyme 6 (EC 6.2.1.45)	protein	990	43% helix, 17% strand	A0AVT1

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 3 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 8 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	390	0.76	0.85	51	GOL, CA
2	746	0.69	0.77	73	ATP, MG, CA
3	467	0.68	0.80	47	ATP, MG, CA
4	377	0.63	0.78	47	GOL
5	408	0.62	0.77	51	GOL

Interfaces

1 interface between chains.

A–B · 583 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (artifact).

Compared structures

7PVN · Crystal Structure of Human UBA6 in Complex with ATP · the same entry in another collection · chain A against A, TM-score 1.00
A0AVT1 · AlphaFold monomer V2.0 prediction for ubiquitin-like modifier- activating enzyme 6… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 A0AVT1
Elsewhere: RCSB PDB 7PVN · PDBe 7PVN · UniProt A0AVT1

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