MolNFT v1 · #121435 · protein
Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1
5HVK · Lim domain kinase 1: “Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1”. X-ray diffraction, 2 ligands (ANP, MG), 12 pockets (best druggability 0.79). MolNFT v1 #121435 on GenesisL1: 3D structure, binding…
- PDB
- 5HVK
- Type
- protein
- Length
- 919 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lim domain kinase 1; Cofilin-1
- EC
- 2.7.11.1
- UniProt
- P53667, P23528
- Ligands
- ANP, MG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lim domain kinase 1 (EC 2.7.11.1) | protein | 298 | 36% helix, 16% strand | P53667 |
| B | Cofilin-1 | protein | 165 | 32% helix, 29% strand | P23528 |
| C | Lim domain kinase 1 (EC 2.7.11.1) | protein | 292 | 38% helix, 16% strand | P53667 |
| D | Cofilin-1 | protein | 164 | 32% helix, 30% strand | P23528 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.79 | 0.82 | 70 | ANP, MG |
| 2 | 740 | 0.77 | 0.81 | 73 | ANP, MG |
| 3 | 725 | 0.68 | 0.76 | 74 | empty |
| 4 | 248 | 0.46 | 0.73 | 41 | empty |
| 5 | 193 | 0.44 | 0.74 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 993 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 921 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 350 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 345 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 85 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 5HVK · Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1 · the same entry in another collection · chain D against D, TM-score 1.00
- P53667 · AlphaFold monomer V2.0 prediction for lim domain kinase 1 (P53667) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P23528 · AlphaFold monomer V2.0 prediction for cofilin-1 (P23528) · a predicted model of the same protein · chain B 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 P53667
- Every structure of UniProt P23528
- Elsewhere: RCSB PDB 5HVK · PDBe 5HVK · UniProt P53667 · UniProt P23528
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