5QU2: Human Nck SH3.1

Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY. Determined by X-ray diffraction at 1.04 Å resolution. Released 12 Feb 2020.

Method: X-ray diffraction
Resolution: 1.04 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 1,364
Mol. weight: 16.73 kDa
Released: 12 Feb 2020

Explore 5QU2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5QU2 contains 4 α-helices and 16 β-strands across 4 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: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	11	1	2
β-strand	18	1	1
β-strand	21	1	2
β-strand	26-31	6	1
β-strand	36-40	5	1
β-strand	46-50	5	1
α-helix	51-53	3
β-strand	54-56	3	1

Chain B: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	3
β-strand	11	1	4
β-strand	18	1	3
β-strand	21	1	4
β-strand	26-31	6	3
β-strand	36-40	5	3
β-strand	46-50	5	3
α-helix	51-53	3
β-strand	54-55	2	3

Chains D and E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	181-186	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoplasmic protein NCK1	A, B	protein	60	Homo sapiens	P16333 (AlphaFold model)
Ace-pro-pro-pro-val-pro-asn-pro-asp-tyr-NH2	D, E	protein	11	synthetic construct	P07766 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5QU2_1 Cytoplasmic protein NCK1 (chains A, B)
SMAEEVVVVAKFDYVAQQEQELDIKKNERLWLLDDSKSWWRVRNSMNKTGFVPSNYVERK

Sequence of entity 2 (D, E), FASTA

>5QU2_2 ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2 (chains D, E)
XPPPVPNPDYX

Primary citation

Small molecule AX-024 reduces T cell proliferation independently of CD3ε/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain. Richter, K., Rufer, A.C., Muller, M. et al. J Biol Chem (2020) 295:7849-7864. DOI 10.1074/jbc.RA120.012788 · PubMed

Other PDB entries of the same protein (UniProt P16333 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5QU8 0.93 Å, Crystal Structure of symmetric swapped human Nck SH3.1 domain, 0.93A, orthorhombic form IV
5QU3 1.02 Å, Crystal Structure of domain swapped human Nck SH3.1, 1.01A, monoclinic
5QU4 1.05 Å, Crystal Structure of swapped human Nck SH3.1 domain, 1.05A, orthorhombic form I
5QU1 1.08 Å, Crystal Structure of the monomeric human Nck SH3.1 domain, triclinic, 1.08A
5QU5 1.11 Å, Domain Swap in the first SH3 domain of human Nck1
5QU7 1.27 Å, Crystal Structure of swapped human Nck SH3.1 domain, 1.3A, orthorhombic form III
2CI9 1.5 Å, Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir
5QUA 1.51 Å, Crystal Structure of swapped human Nck SH3.1 domain, 1.5A, C2221
2CI8 1.8 Å, sh2 domain of human nck1 adaptor protein - uncomplexed
5QU6 1.82 Å, Crystal Structure of swapped human Nck SH3.1 domain, 1.8A, triclinic
2CUB Solution structure of the SH3 domain of the human cytoplasmic protein Nck1
2JS0 Solution structure of second SH3 domain of adaptor Nck

Browse structure collections

About this viewer

MolViewer shows 5QU2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.