MolNFT v1 · #102630 · protein
Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer
4ORH · Ubiquitin-conjugating enzyme E2 variant 2: “Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer”. X-ray diffraction, 1 ligand (ZN), 19 pockets (best druggability 0.70). MolNFT v1 #102630 on GenesisL1: 3D structure, binding…
- PDB
- 4ORH
- Type
- protein
- Length
- 1,513 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 variant 2; Ubiquitin-conjugating enzyme E2 N; E3…
- EC
- 6.3.2.19, 6.3.2.-
- UniProt
- Q15819, P61088, O76064
- Ligands
- ZN
- Pockets
- 19 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 variant 2 | protein | 139 | 27% helix, 20% strand | Q15819 |
| B, F, J | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 148 | 34% helix, 18% strand | P61088 |
| C | E3 ubiquitin-protein ligase RNF8 (EC 6.3.2.-) | protein | 92 | 46% helix, 15% strand | O76064 |
| E, I | Ubiquitin-conjugating enzyme E2 variant 2 | protein | 138 | 27% helix, 20% strand | Q15819 |
| G, K | E3 ubiquitin-protein ligase RNF8 (EC 6.3.2.-) | protein | 139 | 65% helix, 10% strand | O76064 |
| H, L | E3 ubiquitin-protein ligase RNF8 (EC 6.3.2.-) | protein | 142 | 65% helix, 10% strand | O76064 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains C, G, H, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.70 | 0.77 | 77 | empty |
| 2 | 661 | 0.69 | 0.77 | 58 | empty |
| 3 | 197 | 0.57 | 0.79 | 32 | empty |
| 4 | 184 | 0.56 | 0.80 | 30 | empty |
| 5 | 193 | 0.55 | 0.79 | 24 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1315 Ų buried · 4 hydrogen bonds · protein-protein
- K–L · 1266 Ų buried · 7 hydrogen bonds · protein-protein
- I–J · 786 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 769 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 757 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ORH · Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer · the same entry in another collection · chain L against L, TM-score 1.00
- Q15819 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 variant 2 (Q15819) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q15819
- Every structure of UniProt P61088
- Every structure of UniProt O76064
- Elsewhere: RCSB PDB 4ORH · PDBe 4ORH · UniProt Q15819 · UniProt P61088 · UniProt O76064
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