Research workbench
X-ray structure of the coiled coil GCN4 acid base heterodimer acid-D12IA16V base-D12LA16L
Analyse X-ray structure of the coiled coil GCN4 acid base heterodimer acid-D12IA16V… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KD8
- Type
- protein
- Length
- 209 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GCN4 acid base heterodimer acid-D12IA16V; GCN4 acid base heterodimer base-D12LA16L
- Ligands
- ACE
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 93% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | GCN4 acid base heterodimer acid-D12IA16V | protein | 35 | 91% helix, 0% strand | — |
| B, D | GCN4 acid base heterodimer base-D12LA16L | protein | 35 | 94% helix, 0% strand | — |
| E | GCN4 acid base heterodimer base-D12LA16L | protein | 34 | 94% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.46 | 0.77 | 20 | empty |
| 2 | 77 | 0.35 | 0.75 | 11 | empty |
Interfaces
5 interfaces between chains.
- E–F · 1008 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 991 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 958 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 308 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 300 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 3 disulfide (covalent ligand, disulfide).
Compared structures
- 1KD8 · X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L · 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
- Elsewhere: RCSB PDB 1KD8 · PDBe 1KD8
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