MolNFT v1 · #44116 · protein
NMR structure of two domains in ubiquitin ligase GP78, ring and G2BR, bound to its conjugating enzyme UBE2G
2LXP · Ubiquitin-conjugating enzyme E2 G2: “NMR structure of two domains in ubiquitin ligase GP78, ring and G2BR, bound to its conjugating enzyme UBE2G”. Solution nmr, 1 ligand (ZN), 1 pocket (best druggability 0.32). MolNFT v1 #44116 on…
- PDB
- 2LXP
- Type
- protein
- Length
- 241 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 G2; E3 ubiquitin-protein ligase amfr
- EC
- 6.3.2.19, 6.3.2.-
- UniProt
- P60604, Q9UKV5
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.32
Structure
solution nmr · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 G2 (EC 6.3.2.19) | protein | 156 | 35% helix, 20% strand | P60604 |
| B | E3 ubiquitin-protein ligase amfr (EC 6.3.2.-) | protein | 27 | 85% helix, 0% strand | Q9UKV5 |
| C | E3 ubiquitin-protein ligase amfr (EC 6.3.2.-) | protein | 58 | 28% helix, 21% strand | Q9UKV5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.32 | 0.77 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1018 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 677 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2LXP · NMR structure of two domains in ubiquitin ligase gp78, RING and G2BR, bound to its… · the same entry in another collection · chain A against A, TM-score 1.00
- P60604 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 G2 (P60604) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q9UKV5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase amfr (Q9UKV5) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 P60604
- Every structure of UniProt Q9UKV5
- Elsewhere: RCSB PDB 2LXP · PDBe 2LXP · UniProt P60604 · UniProt Q9UKV5
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