Research workbench
Dimeric structure of dapk-1 catalytic domain in complex with amppcp-mg
Analyse Dimeric structure of dapk-1 catalytic domain in complex with amppcp-mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZXT
- Type
- protein
- Length
- 1,006 residues
- Chains
- 4
- 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
- ACP, MG
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 1 (EC 2.7.11.1) | protein | 249 | 37% helix, 20% strand | P53355 |
| B | Death-associated protein kinase 1 (EC 2.7.11.1) | protein | 253 | 35% helix, 21% strand | P53355 |
| C | Death-associated protein kinase 1 (EC 2.7.11.1) | protein | 259 | 37% helix, 17% strand | P53355 |
| D | Death-associated protein kinase 1 (EC 2.7.11.1) | protein | 245 | 38% helix, 17% strand | P53355 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.65 | 0.78 | 42 | MG, ACP |
| 2 | 321 | 0.63 | 0.79 | 41 | ACP, MG |
| 3 | 330 | 0.61 | 0.78 | 36 | MG, ACP |
| 4 | 306 | 0.60 | 0.78 | 40 | ACP, MG |
| 5 | 186 | 0.51 | 0.77 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1439 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1416 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 270 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3ZXT · Dimeric structure of DAPK-1 catalytic domain in complex with AMPPCP- Mg · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.95
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 3ZXT · PDBe 3ZXT · UniProt P53355
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.