MolNFT v1 · #121434 · protein
Crystal structure of LIMK1 D460N mutant in complex with AMP-pnp
5HVJ · Lim domain kinase 1: “Crystal structure of LIMK1 D460N mutant in complex with AMP-pnp”. X-ray diffraction, 1 ligand (ANP), 5 pockets (best druggability 0.66). MolNFT v1 #121434 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5HVJ
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lim domain kinase 1
- EC
- 2.7.11.1
- UniProt
- P53667
- Ligands
- ANP
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lim domain kinase 1 (EC 2.7.11.1) | protein | 283 | 39% helix, 17% strand | P53667 |
| B | Lim domain kinase 1 (EC 2.7.11.1) | protein | 284 | 36% helix, 14% strand | P53667 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.66 | 0.83 | 43 | empty |
| 2 | 486 | 0.65 | 0.77 | 48 | empty |
| 3 | 421 | 0.64 | 0.78 | 41 | ANP |
| 4 | 57 | 0.36 | 0.78 | 12 | empty |
| 5 | 69 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 426 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 P53667
- Elsewhere: RCSB PDB 5HVJ · PDBe 5HVJ · UniProt P53667
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