Research workbench
N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: structure of a human CUL1WHB- DCN1P-acetylated UBC12N complex
Analyse N-terminal acetylation acts as an avidity enhancer within an interconnected… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TDU
- Type
- protein
- Length
- 568 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DCN1-like protein 1; Cullin-1; NEDD8-conjugating enzyme UBC12
- EC
- 6.3.2.-
- UniProt
- Q96GG9, Q13616, P61081
- Ligands
- ACE
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DCN1-like protein 1 | protein | 193 | 61% helix, 7% strand | Q96GG9 |
| B | DCN1-like protein 1 | protein | 194 | 61% helix, 5% strand | Q96GG9 |
| C | Cullin-1 | protein | 75 | 60% helix, 19% strand | Q13616 |
| D | Cullin-1 | protein | 76 | 59% helix, 18% strand | Q13616 |
| E, F | NEDD8-conjugating enzyme UBC12 (EC 6.3.2.-) | protein | 15 | 73% helix, 0% strand | P61081 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, E, A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.80 | 0.85 | 68 | empty |
| 2 | 703 | 0.77 | 0.82 | 73 | empty |
| 3 | 70 | 0.36 | 0.77 | 13 | empty |
| 4 | 64 | 0.31 | 0.75 | 20 | empty |
| 5 | 60 | 0.28 | 0.74 | 24 | empty |
Interfaces
7 interfaces between chains.
- A–C · 648 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 629 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 617 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 611 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 582 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3TDU · N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein… · the same entry in another collection · chain F against F, TM-score 1.00
- Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q96GG9 · AlphaFold monomer V2.0 prediction for DCN1-like protein 1 (Q96GG9) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P61081 · AlphaFold monomer V2.0 prediction for NEDD8-conjugating enzyme UBC12 (P61081) · a predicted model of the same protein · chain E against A, TM-score 0.67
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 Q96GG9
- Every structure of UniProt Q13616
- Every structure of UniProt P61081
- Elsewhere: RCSB PDB 3TDU · PDBe 3TDU · UniProt Q96GG9 · UniProt Q13616 · UniProt P61081
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