MolNFT v2 · #187479 · protein

Ubiquitin variant UbV.k.2 in complex with Ube2k

7MYH · Ubiquitin-conjugating enzyme E2 K: “Ubiquitin variant UbV.k.2 in complex with Ube2k”. X-ray diffraction at 2.394, 2 pockets (best druggability 0.32). MolNFT v2 #187479 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7MYH
Type: protein
Length: 274 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.394
Source: Homo sapiens
Molecule: Ubiquitin-conjugating enzyme E2 K; Ubiquitin variant UbV.k.2
EC: 2.3.2.23
UniProt: P61086, P0CG47
Pockets: 2 · best druggability 0.32

Structure

x-ray diffraction · resolution 2.394 · 2 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-conjugating enzyme E2 K (EC 2.3.2.23)	protein	200	45% helix, 13% strand	P61086
B	Ubiquitin variant UbV.k.2	protein	74	20% helix, 34% strand	P0CG47

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	52	0.32	0.77	16	empty
2	54	0.30	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 558 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7MYH · Ubiquitin variant UBV.K.2 in complex with UBE2K · the same entry in another collection · chain A against A, TM-score 1.00
P61086 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 K (P61086) · 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 P61086
Every structure of UniProt P0CG47
Elsewhere: RCSB PDB 7MYH · PDBe 7MYH · UniProt P61086 · UniProt P0CG47

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