Research workbench
APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP
Analyse APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R4N
- Type
- protein
- Length
- 4,040 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid beta precursor protein-binding protein 1; Ubiquitin-activating enzyme E1C…
- UniProt
- Q13564, Q8TBC4, Q15843
- Ligands
- ATP, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Amyloid beta precursor protein-binding protein 1 | protein | 516 | 52% helix, 9% strand | Q13564 |
| B, D, F, H | Ubiquitin-activating enzyme E1C | protein | 418 | 36% helix, 15% strand | Q8TBC4 |
| I, J, K, L | Ubiquitin-like protein NEDD8 | protein | 76 | 24% helix, 28% strand | Q15843 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, I, C, D, J, E, F, K, G, H, L
- ZN · Zinc ion · metal · 4 copies · chains D, J, 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 | 929 | 0.83 | 0.85 | 91 | empty |
| 2 | 965 | 0.81 | 0.83 | 84 | empty |
| 3 | 957 | 0.76 | 0.79 | 114 | empty |
| 4 | 1007 | 0.74 | 0.77 | 90 | ATP |
| 5 | 567 | 0.74 | 0.82 | 72 | empty |
Interfaces
20 interfaces between chains.
- E–F · 3649 Ų buried · 50 hydrogen bonds · protein-protein
- G–H · 3640 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 3629 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 3627 Ų buried · 49 hydrogen bonds · protein-protein
- H–L · 1258 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1R4N · APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP · the same entry in another collection · chain A against A, 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 1R4N · PDBe 1R4N · UniProt Q13564 · UniProt Q8TBC4 · UniProt Q15843
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