Research workbench
NMR structure of two domains in ubiquitin ligase GP78, ring and G2BR, bound to its conjugating enzyme UBE2G
Analyse NMR structure of two domains in ubiquitin ligase GP78, ring and G2BR, bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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