MolNFT v1 · #104931 · protein
Crystal structure of RNF146(RING-WWE)/UBCH5A/ISO-adpr complex
4QPL · E3 ubiquitin-protein ligase RNF146: “Crystal structure of RNF146(RING-WWE)/UBCH5A/ISO-adpr complex”. X-ray diffraction, 2 ligands (V3L, ZN), 12 pockets (best druggability 0.67). MolNFT v1 #104931 on GenesisL1: 3D structure, binding…
- PDB
- 4QPL
- Type
- protein
- Length
- 608 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF146; Ubiquitin-conjugating enzyme E2 D1
- EC
- 6.3.2.-, 6.3.2.19
- UniProt
- Q9CZW6, P51668
- Ligands
- V3L, ZN
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | E3 ubiquitin-protein ligase RNF146 (EC 6.3.2.-) | protein | 153 | 18% helix, 31% strand | Q9CZW6 |
| B | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 149 | 38% helix, 21% strand | P51668 |
| D | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 153 | 37% helix, 20% strand | P51668 |
Ligands and binding sites
- V3L · 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.67 | 0.84 | 27 | empty |
| 2 | 217 | 0.66 | 0.84 | 25 | empty |
| 3 | 132 | 0.55 | 0.82 | 19 | V3L |
| 4 | 165 | 0.54 | 0.80 | 26 | V3L |
| 5 | 116 | 0.49 | 0.80 | 30 | empty |
Interfaces
3 interfaces between chains.
- C–D · 755 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 730 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 648 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4QPL · Crystal structure of RNF146(RING-WWE)/UbcH5a/iso-ADPr complex · the same entry in another collection · chain A against A, TM-score 1.00
- P51668 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D1 (P51668) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q9CZW6 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF146 (Q9CZW6) · a predicted model of the same protein · chain A 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 Q9CZW6
- Every structure of UniProt P51668
- Elsewhere: RCSB PDB 4QPL · PDBe 4QPL · UniProt Q9CZW6 · UniProt P51668
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