MolNFT v1 · #12320 · protein
X-ray structure of the coiled coil GCN4 acid base heterodimer acid-D12LA16L base-D12LA16L
1KD9: “X-ray structure of the coiled coil GCN4 acid base heterodimer acid-D12LA16L base-D12LA16L”. X-ray diffraction, 1 ligand (ACE), 3 pockets (best druggability 0.45). MolNFT v1 #12320 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1KD9
- Type
- protein
- Length
- 208 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GCN4 acid base heterodimer acid-D12LA16L; GCN4 acid base heterodimer base-D12LA16L
- Ligands
- ACE
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 94% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | GCN4 acid base heterodimer acid-D12LA16L | protein | 35 | 94% helix, 0% strand | — |
| B | GCN4 acid base heterodimer base-D12LA16L | protein | 35 | 94% helix, 0% strand | — |
| D, E | GCN4 acid base heterodimer base-D12LA16L | protein | 34 | 94% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 5 copies · chains A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.45 | 0.76 | 20 | empty |
| 2 | 150 | 0.42 | 0.74 | 21 | empty |
| 3 | 87 | 0.35 | 0.74 | 10 | empty |
Interfaces
5 interfaces between chains.
- E–F · 1003 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 1001 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 966 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 261 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 163 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 covalent, 3 disulfide (covalent ligand, disulfide).
Compared structures
- 1KD9 · X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L 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 1KD9 · PDBe 1KD9
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