Research workbench
Structural dissection of a gating mechanism preventing misactivation of ubiquitin by NEDD8'S E1 (APPBP1-UBA3ARG190ALA-NEDD8ALA72ARG)
Analyse Structural dissection of a gating mechanism preventing misactivation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DBH
- Type
- protein
- Length
- 4,123 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NEDD8-activating enzyme E1 regulatory subunit; NEDD8-activating enzyme E1 catalytic…
- EC
- 6.3.2.-
- UniProt
- Q13564, Q8TBC4, Q15843
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NEDD8-activating enzyme E1 regulatory subunit | protein | 522 | 51% helix, 10% strand | Q13564 |
| B, D | NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) | protein | 432 | 36% helix, 18% strand | Q8TBC4 |
| I | NEDD8 | protein | 86 | 22% helix, 27% strand | Q15843 |
| C | NEDD8-activating enzyme E1 regulatory subunit | protein | 520 | 52% helix, 10% strand | Q13564 |
| J, K, L | NEDD8 | protein | 76 | 20% helix, 28% strand | Q15843 |
| E | NEDD8-activating enzyme E1 regulatory subunit | protein | 523 | 54% helix, 10% strand | Q13564 |
| F, H | NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) | protein | 431 | 35% helix, 13% strand | Q8TBC4 |
| G | NEDD8-activating enzyme E1 regulatory subunit | protein | 518 | 51% helix, 10% strand | Q13564 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.82 | 0.83 | 99 | empty |
| 2 | 1143 | 0.81 | 0.82 | 108 | empty |
| 3 | 104 | 0.79 | 0.98 | 26 | empty |
| 4 | 841 | 0.76 | 0.80 | 100 | empty |
| 5 | 775 | 0.75 | 0.80 | 92 | empty |
Interfaces
20 interfaces between chains.
- G–H · 3637 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 3634 Ų buried · 55 hydrogen bonds · protein-protein
- E–F · 3631 Ų buried · 62 hydrogen bonds · protein-protein
- C–D · 3617 Ų buried · 61 hydrogen bonds · protein-protein
- D–J · 1379 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3DBH · Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by… · the same entry in another collection · chain L against L, TM-score 1.00
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 Q13564
- Every structure of UniProt Q8TBC4
- Every structure of UniProt Q15843
- Elsewhere: RCSB PDB 3DBH · PDBe 3DBH · UniProt Q13564 · UniProt Q8TBC4 · UniProt Q15843
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.