5L7K: Myristoylated NPHP3 peptide

The crystal structure of myristoylated NPHP3 peptide in complex with UNC119a. Determined by X-ray diffraction at 2.1 Å resolution. Released 10 Aug 2016.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,781
Mol. weight: 43.31 kDa
Ligands: MYR
Released: 10 Aug 2016

Explore 5L7K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L7K contains 11 α-helices and 18 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	62-65	4
α-helix	79-81	3
β-strand	87-95	9	1
β-strand	101-106	6	1
β-strand	128-132	5	2
α-helix	135-139	5
β-strand	142-150	9	1
β-strand	156-167	12	2
β-strand	170-182	13	2
β-strand	187-195	9	1
α-helix	196-198	3
α-helix	201-209	9
β-strand	214-222	9	2
β-strand	225-235	11	2

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4

Chain G: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	62-65	4
α-helix	79-81	3
β-strand	87-95	9	3
β-strand	101-106	6	3
β-strand	129-132	4	4
α-helix	135-139	5
β-strand	142-150	9	3
β-strand	156-167	12	4
β-strand	171-182	12	4
β-strand	187-195	9	3
α-helix	196-198	3
α-helix	201-209	9
β-strand	214-222	9	4
β-strand	225-235	11	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein unc-119 homolog A	A, G	protein	180	Homo sapiens	Q13432 (AlphaFold model)
Gly-thr-ala-ser-ser-leu	B	protein	6	Homo sapiens	Q7Z494 (AlphaFold model)

Sequence of entity 1 (A, G), FASTA

>5L7K_1 Protein unc-119 homolog A (chains A, G)
QPIGPEDVLGLQRITGDYLCSPEENIYKIDFVRFKIRDMDSGTVLFEIKKPPVSERLPIN
RRDLDPNAGRFVRYQFTPAFLRLRQVGATVEFTVGDKPVNNFRMIERHYFRNQLLKSFDF
HFGFCIPSSKNTCEHIYDFPPLSEELISEMIRHPYETQSDSFYFVDDRLVMHNKADYSYS

Sequence of entity 2 (B), FASTA

>5L7K_2 GLY-THR-ALA-SER-SER-LEU (chains B)
GTASSL

Ligands and cofactors

ID	Name	Formula	Copies
MYR	Myristic acid	C14 H28 O2	1

Primary citation

Novel Biochemical and Structural Insights into the Interaction of Myristoylated Cargo with Unc119 Protein and Their Release by Arl2/3. Jaiswal, M., Fansa, E.K., Kosling, S.K. et al. J Biol Chem (2016) 291:20766-20778. DOI 10.1074/jbc.M116.741827 · PubMed

Other PDB entries of the same protein (UniProt Q13432 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3GQQ 1.95 Å, Crystal structure of the human retinal protein 4 (unc-119 homolog A). Northeast…
3RBQ 2.0 Å, Co-crystal structure of human UNC119 (retina gene 4) and an N-terminal Transducin-alpha…
6H6A 2.0 Å, Crystal structure of UNC119 in complex with LCK peptide
4GOJ 2.1 Å, The Crystal Structure of full length Arl3GppNHp in complex with UNC119a
9GKG 2.21 Å, Crystal structure of UNC119 in complex with Squarunkin A
7UMO 2.3 Å, Structure of Unc119-inhibitor complex.
9NEM 2.49 Å, Structure of Unc119-Farnesylated peptide complex
4GOK 2.6 Å, The Crystal structure of Arl2GppNHp in complex with UNC119a

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