MolNFT v1 · #70506 · protein
Crystal structure of the inactive alpha-kinase domain of myosin heavy chain kinase a (D766A) complex with ATP
3LMI: “Crystal structure of the inactive alpha-kinase domain of myosin heavy chain kinase a (D766A) complex with ATP”. X-ray diffraction, 4 ligands (ATP, ZN, MG), 15 pockets (best druggability 0.78). MolNFT v1 #70506 on GenesisL1: 3D…
- PDB
- 3LMI
- Type
- protein
- Length
- 1,003 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin heavy chain kinase a
- EC
- 2.7.11.7
- UniProt
- P42527
- Ligands
- ATP, ZN, MG, PO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin heavy chain kinase a (EC 2.7.11.7) | protein | 246 | 25% helix, 29% strand | P42527 |
| B | Myosin heavy chain kinase a (EC 2.7.11.7) | protein | 254 | 24% helix, 28% strand | P42527 |
| C | Myosin heavy chain kinase a (EC 2.7.11.7) | protein | 250 | 24% helix, 28% strand | P42527 |
| D | Myosin heavy chain kinase a (EC 2.7.11.7) | protein | 253 | 23% helix, 28% strand | P42527 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.78 | 0.80 | 90 | empty |
| 2 | 858 | 0.78 | 0.81 | 87 | empty |
| 3 | 898 | 0.75 | 0.79 | 83 | empty |
| 4 | 525 | 0.70 | 0.79 | 66 | MG, ATP |
| 5 | 310 | 0.64 | 0.80 | 37 | MG, ATP |
Interfaces
3 interfaces between chains.
- A–B · 1038 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1036 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 389 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3LMI · Crystal Structure of the Inactive Alpha-kinase Domain of Myosin Heavy Chain Kinase A… · the same entry in another collection · chain D against D, TM-score 1.00
- P42527 · AlphaFold monomer V2.0 prediction for myosin heavy chain kinase a (P42527) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P42527
- Elsewhere: RCSB PDB 3LMI · PDBe 3LMI · UniProt P42527
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