Research workbench
The crystal structure of myristoylated NPHP3 peptide in complex with UNC119A
Analyse The crystal structure of myristoylated NPHP3 peptide in complex with UNC119A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L7K
- Type
- protein
- Length
- 327 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein unc-119 homolog a; Gly-thr-ala-ser-ser-leu
- UniProt
- Q13432
- Ligands
- MYR
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein unc-119 homolog a | protein | 161 | 13% helix, 52% strand | Q13432 |
| B | Gly-thr-ala-ser-ser-leu | protein | 6 | 67% helix, 0% strand | — |
| G | Protein unc-119 homolog a | protein | 160 | 13% helix, 51% strand | Q13432 |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.81 | 0.97 | 22 | MYR |
| 2 | 313 | 0.76 | 0.87 | 44 | empty |
| 3 | 224 | 0.53 | 0.77 | 29 | empty |
| 4 | 167 | 0.52 | 0.79 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–G · 481 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 473 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 5L7K · The crystal structure of myristoylated NPHP3 peptide in complex with UNC119a · the same entry in another collection · chain A against A, TM-score 1.00
- Q13432 · AlphaFold monomer V2.0 prediction for protein unc-119 homolog a (Q13432) · a predicted model of the same protein · chain G against A, TM-score 0.98
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 Q13432
- Elsewhere: RCSB PDB 5L7K · PDBe 5L7K · UniProt Q13432
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