Research workbench
Dcnl complex with N-terminally acetylated NEDD8 E2 peptide
Analyse Dcnl complex with N-terminally acetylated NEDD8 E2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GAO
- Type
- protein
- Length
- 807 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DCN1-like protein 2; NEDD8-conjugating enzyme UBC12
- UniProt
- Q6PH85, P61081
- Ligands
- BR
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | DCN1-like protein 2 | protein | 193 | 61% helix, 7% strand | Q6PH85 |
| B | DCN1-like protein 2 | protein | 192 | 63% helix, 4% strand | Q6PH85 |
| C, E, H | NEDD8-conjugating enzyme UBC12 | protein | 10 | 60% helix, 0% strand | P61081 |
| D | DCN1-like protein 2 | protein | 188 | 59% helix, 5% strand | Q6PH85 |
| F | NEDD8-conjugating enzyme UBC12 | protein | 11 | 55% helix, 0% strand | P61081 |
Ligands and binding sites
- BR · Bromide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.55 | 0.75 | 52 | empty |
| 2 | 164 | 0.49 | 0.77 | 20 | empty |
| 3 | 149 | 0.41 | 0.74 | 35 | empty |
| 4 | 161 | 0.40 | 0.73 | 27 | empty |
| 5 | 135 | 0.38 | 0.73 | 24 | empty |
Interfaces
8 interfaces between chains.
- D–E · 528 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 488 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 484 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 427 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
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 Q6PH85
- Every structure of UniProt P61081
- Elsewhere: RCSB PDB 4GAO · PDBe 4GAO · UniProt Q6PH85 · UniProt P61081
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