MolNFT v1 · #170270 · protein
DDR1 kinase autoinhibited by its juxtamembrane region
6Y23 · Epithelial discoidin domain-containing receptor 1: “DDR1 kinase autoinhibited by its juxtamembrane region”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.80). MolNFT v1 #170270 on GenesisL1: 3D structure, binding…
- PDB
- 6Y23
- Type
- protein
- Length
- 911 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epithelial discoidin domain-containing receptor 1
- EC
- 2.7.10.1
- UniProt
- Q08345
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 305 | 39% helix, 18% strand | Q08345 |
| B | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 301 | 38% helix, 17% strand | Q08345 |
| C | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 305 | 39% helix, 17% strand | Q08345 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.80 | 0.81 | 110 | empty |
| 2 | 527 | 0.71 | 0.80 | 57 | SO4 |
| 3 | 125 | 0.43 | 0.76 | 22 | empty |
| 4 | 97 | 0.41 | 0.77 | 18 | empty |
| 5 | 93 | 0.39 | 0.76 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–C · 765 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 645 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Y23 · DDR1 kinase autoinhibited by its juxtamembrane region · the same entry in another collection · chain A against A, TM-score 1.00
- Q08345 · AlphaFold monomer V2.0 prediction for epithelial discoidin domain- containing receptor 1… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q08345
- Elsewhere: RCSB PDB 6Y23 · PDBe 6Y23 · UniProt Q08345
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