MolNFT v1 · #146068 · protein
UBE2V1 in complex with ubiquitin variant UBV.V1.1 and UBE2N/UBC13
6D6I · Ubiquitin-conjugating enzyme E2 variant 1: “UBE2V1 in complex with ubiquitin variant UBV.V1.1 and UBE2N/UBC13”. X-ray diffraction, 8 pockets (best druggability 0.73). MolNFT v1 #146068 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6D6I
- Type
- protein
- Length
- 697 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 variant 1; Ubiquitin-conjugating enzyme E2 N; UBV.V1.1
- EC
- 2.3.2.23
- UniProt
- Q13404, P61088, Q96H31
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ubiquitin-conjugating enzyme E2 variant 1 | protein | 136 | 26% helix, 22% strand | Q13404 |
| B | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 139 | 35% helix, 14% strand | P61088 |
| C, F | UBV.V1.1 | protein | 73 | 22% helix, 33% strand | Q96H31 |
| E | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 140 | 35% helix, 14% strand | P61088 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.73 | 0.85 | 64 | empty |
| 2 | 570 | 0.67 | 0.77 | 55 | empty |
| 3 | 194 | 0.65 | 0.84 | 29 | empty |
| 4 | 104 | 0.56 | 0.84 | 28 | empty |
| 5 | 122 | 0.55 | 0.82 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–D · 904 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 850 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 831 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 599 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 589 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6D6I · Ube2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13 · the same entry in another collection · chain F against F, TM-score 1.00
- Q13404 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 variant 1 (Q13404) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q13404
- Every structure of UniProt P61088
- Every structure of UniProt Q96H31
- Elsewhere: RCSB PDB 6D6I · PDBe 6D6I · UniProt Q13404 · UniProt P61088 · UniProt Q96H31
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