Research workbench
RCR E3 ligase E2-Ubiquitin transthiolation intermediate
Analyse RCR E3 ligase E2-Ubiquitin transthiolation intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T7F
- Type
- protein
- Length
- 471 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.58
- Source
- Homo sapiens
- Molecule
- E3 ubiquitin-protein ligase MYCBP2; Ubiquitin-conjugating enzyme E2 D3; Polyubiquitin-C
- EC
- 2.3.2.-, 2.3.2.23, 2.3.2.24
- UniProt
- O75592, P61077, P0CG48
- Ligands
- LWZ, ZN
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.58 · 3 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MYCBP2 (EC 2.3.2.-) | protein | 250 | 33% helix, 16% strand | O75592 |
| B | Ubiquitin-conjugating enzyme E2 D3 (EC 2.3.2.23, 2.3.2.24) | protein | 150 | 37% helix, 18% strand | P61077 |
| C | Polyubiquitin-C | protein | 71 | 21% helix, 31% strand | P0CG48 |
Ligands and binding sites
- LWZ · 3,3-bis(sulfanyl)-~{N}-(1~{H}-1,2,3-triazol-4-ylmethyl)propanamide · ligand · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.81 | 0.83 | 101 | LWZ |
| 2 | 56 | 0.66 | 0.95 | 22 | empty |
| 3 | 68 | 0.64 | 0.92 | 28 | empty |
| 4 | 234 | 0.54 | 0.77 | 34 | empty |
| 5 | 158 | 0.45 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 980 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 577 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 247 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6T7F · Rcr E3 ligase E2-ubiquitin transthiolation intermediate · the same entry in another collection · chain A against A, TM-score 1.00
- P61077 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D3 (P61077) · 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 O75592
- Every structure of UniProt P61077
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6T7F · PDBe 6T7F · UniProt O75592 · UniProt P61077 · UniProt P0CG48
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