MolNFT v1 · #86046 · protein
Structure of BIRC7-UBCH5B-ub complex.
4AUQ · Ubiquitin-conjugating enzyme E2 D2: “Structure of BIRC7-UBCH5B-ub complex.”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.71). MolNFT v1 #86046 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4AUQ
- Type
- protein
- Length
- 558 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; Baculoviral iap repeat-containing protein 7…
- EC
- 6.3.2.19, 6.3.2.-
- UniProt
- P62837, Q96CA5, P0CG48
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 146 | 36% helix, 18% strand | P62837 |
| B, E | Baculoviral iap repeat-containing protein 7 (EC 6.3.2.-) | protein | 57 | 18% helix, 26% strand | Q96CA5 |
| C | Polyubiquitin-C | protein | 77 | 23% helix, 36% strand | P0CG48 |
| F | Polyubiquitin-C | protein | 75 | 20% helix, 32% strand | P0CG48 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.71 | 0.79 | 71 | empty |
| 2 | 272 | 0.63 | 0.81 | 34 | empty |
| 3 | 164 | 0.62 | 0.84 | 38 | empty |
| 4 | 58 | 0.31 | 0.76 | 16 | empty |
| 5 | 58 | 0.29 | 0.75 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–C · 931 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 894 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 752 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 500 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 463 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4AUQ · Structure of BIRC7-UbcH5b-Ub complex. · the same entry in another collection · chain F against F, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q96CA5 · AlphaFold monomer V2.0 prediction for baculoviral iap repeat- containing protein 7… · a predicted model of the same protein · chain E against A, TM-score 0.93
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 P62837
- Every structure of UniProt Q96CA5
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 4AUQ · PDBe 4AUQ · UniProt P62837 · UniProt Q96CA5 · UniProt P0CG48
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.