MolNFT v1 · #146058 · protein

UBE2G1 in complex with ubiquitin variant UBV.G1.1

6D68 · Ubiquitin-conjugating enzyme E2 G1: “UBE2G1 in complex with ubiquitin variant UBV.G1.1”. X-ray diffraction, 4 pockets (best druggability 0.69). MolNFT v1 #146058 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6D68
Type: protein
Length: 465 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-conjugating enzyme E2 G1; UBV.G1.1
EC: 2.3.2.23
UniProt: P62253, Q96H31
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-conjugating enzyme E2 G1 (EC 2.3.2.23)	protein	159	40% helix, 16% strand	P62253
B	Ubiquitin-conjugating enzyme E2 G1 (EC 2.3.2.23)	protein	157	39% helix, 20% strand	P62253
C	UBV.G1.1	protein	75	20% helix, 36% strand	Q96H31
D	UBV.G1.1	protein	74	24% helix, 36% strand	Q96H31

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	667	0.69	0.77	58	empty
2	56	0.37	0.80	16	empty
3	62	0.34	0.77	15	empty
4	96	0.33	0.73	19	empty

Interfaces

5 interfaces between chains.

C–D · 1817 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 867 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 787 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 384 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 362 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (artifact).

Compared structures

6D68 · Ube2G1 in complex with ubiquitin variant Ubv.G1.1 · the same entry in another collection · chain A against A, TM-score 1.00
P62253 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 G1 (P62253) · 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 P62253
Every structure of UniProt Q96H31
Elsewhere: RCSB PDB 6D68 · PDBe 6D68 · UniProt P62253 · UniProt Q96H31

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