MolNFT v1 · #113870 · protein
Crystal structure of DAPK1-kaempferol complex in the presence of iodide ions.
5AV3 · Death-associated protein kinase 1: “Crystal structure of DAPK1-kaempferol complex in the presence of iodide ions.”. X-ray diffraction, 2 ligands (KMP, IOD), 2 pockets (best druggability 0.69). MolNFT v1 #113870 on GenesisL1: 3D…
- PDB
- 5AV3
- Type
- protein
- Length
- 275 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death-associated protein kinase 1
- EC
- 2.7.11.1
- UniProt
- P53355
- Ligands
- KMP, IOD
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 1 (EC 2.7.11.1) | protein | 275 | 34% helix, 20% strand | P53355 |
Ligands and binding sites
- KMP · 3,5,7-trihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one · ligand · chains A
- IOD · Iodide ion · ion · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.69 | 0.80 | 50 | KMP, IOD |
| 2 | 55 | 0.29 | 0.75 | 13 | IOD |
Compared structures
- 5AV3 · Crystal structure of DAPK1-kaempferol complex in the presence of iodide ions. · the same entry in another collection · chain A against A, TM-score 1.00
- P53355 · AlphaFold monomer V2.0 prediction for death-associated protein kinase 1 (P53355) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P53355
- Elsewhere: RCSB PDB 5AV3 · PDBe 5AV3 · UniProt P53355
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