MolNFT v1 · #188918 · protein
Complex of UBE2O with NAP1L1 and ubiquitylated UL2
7UN3 · UBIQUITIN,60S ribosomal protein L8,(E3-independent) E2…: “Complex of UBE2O with NAP1L1 and ubiquitylated UL2”. Electron microscopy, 16 pockets (best druggability 0.79). MolNFT v1 #188918 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7UN3
- Type
- protein
- Length
- 1,164 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UBIQUITIN,60S ribosomal protein L8,(E3-independent) E2 ubiquitin-conjugating enzyme…
- EC
- 2.3.2.24
- UniProt
- P62987, Q9C0C9, P55209
- Pockets
- 16 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | UBIQUITIN,60S ribosomal protein L8,(E3-independent) E2 ubiquitin-conjugating enzyme fusion (EC 2.3.2.24) | protein | 73 | 25% helix, 36% strand | P62987 |
| A | UBIQUITIN,60S ribosomal protein L8,(E3-independent) E2 ubiquitin-conjugating enzyme fusion (EC 2.3.2.24) | protein | 649 | 22% helix, 34% strand | Q9C0C9 |
| B | Nucleosome assembly protein 1-like 1 | protein | 223 | 39% helix, 20% strand | P55209 |
| C | Nucleosome assembly protein 1-like 1 | protein | 219 | 41% helix, 22% strand | P55209 |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.79 | 0.80 | 87 | empty |
| 2 | 201 | 0.58 | 0.81 | 41 | empty |
| 3 | 75 | 0.58 | 0.88 | 25 | empty |
| 4 | 247 | 0.55 | 0.77 | 36 | empty |
| 5 | 81 | 0.55 | 0.86 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1969 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 796 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 444 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 267 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7UN3 · Complex of UBE2O with NAP1L1 and ubiquitylated uL2 · the same entry in another collection · chain C against C, TM-score 1.00
- P62987 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P62987) · a predicted model of the same protein · chain D against A, TM-score 0.94
- P55209 · AlphaFold monomer V2.0 prediction for nucleosome assembly protein 1-like 1 (P55209) · a predicted model of the same protein · chain C against A, TM-score 0.94
- Q9C0C9 · AlphaFold monomer V2.0 prediction for (E3-independent) E2 ubiquitin- conjugating enzyme… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P62987
- Every structure of UniProt Q9C0C9
- Every structure of UniProt P55209
- Elsewhere: RCSB PDB 7UN3 · PDBe 7UN3 · UniProt P62987 · UniProt Q9C0C9 · UniProt P55209
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