5QU6: Swapped human Nck SH3.1 domain, 1.8A, triclinic
Crystal Structure of swapped human Nck SH3.1 domain, 1.8A, triclinic. Determined by X-ray diffraction at 1.82 Å resolution. Released 12 Feb 2020.
- Method
- X-ray diffraction
- Resolution
- 1.82 Å
- Organism
- Homo sapiens
- Chains
- 28
- Atoms
- 13,353
- Mol. weight
- 288.38 kDa
- Released
- 12 Feb 2020
Explore 5QU6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5QU6 contains 40 α-helices and 222 β-strands across 28 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 1: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-9 | 4 | 3 |
| β-strand | 14 | 1 | 4 |
| β-strand | 21 | 1 | 3 |
| β-strand | 24 | 1 | 4 |
| β-strand | 29-32 | 4 | 3 |
| β-strand | 39-43 | 5 | 3 |
| β-strand | 49-53 | 5 | 3 |
| α-helix | 54-56 | 3 | |
| β-strand | 57 | 1 | 5 |
Chain 2: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-9 | 4 | 3 |
| β-strand | 10 | 1 | 5 |
| β-strand | 29-32 | 4 | 3 |
| β-strand | 39-43 | 5 | 3 |
| β-strand | 49-53 | 5 | 3 |
| α-helix | 54-56 | 3 | |
Chains A, B, C and D: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-10 | 5 | 1 |
| β-strand | 14 | 1 | 2 |
| β-strand | 21 | 1 | 1 |
| β-strand | 24 | 1 | 2 |
| β-strand | 29-32 | 4 | 1 |
| β-strand | 39-43 | 5 | 1 |
| β-strand | 49-53 | 5 | 1 |
| α-helix | 54-56 | 3 | |
| β-strand | 57-58 | 2 | 1 |
Chain E: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-10 | 6 | 10 |
| β-strand | 14 | 1 | 11 |
| β-strand | 21 | 1 | 10 |
| β-strand | 24 | 1 | 11 |
| β-strand | 29-33 | 5 | 10 |
| β-strand | 39-43 | 5 | 10 |
| β-strand | 49-53 | 5 | 10 |
| α-helix | 54-56 | 3 | |
| β-strand | 57-58 | 2 | 10 |
Chain F: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-10 | 5 | 10 |
| β-strand | 14 | 1 | 12 |
| β-strand | 21 | 1 | 10 |
| β-strand | 24 | 1 | 12 |
| β-strand | 29-32 | 4 | 10 |
| β-strand | 39-43 | 5 | 10 |
| β-strand | 49-53 | 5 | 10 |
| α-helix | 54-56 | 3 | |
| β-strand | 57-59 | 3 | 10 |
Chain G: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-10 | 4 | 13 |
| β-strand | 14 | 1 | 14 |
| β-strand | 21 | 1 | 13 |
| β-strand | 24 | 1 | 14 |
| β-strand | 29-32 | 4 | 13 |
| α-helix | 34-36 | 3 | |
| β-strand | 39-43 | 5 | 13 |
| β-strand | 49-53 | 5 | 13 |
| α-helix | 54-56 | 3 | |
| β-strand | 57-58 | 2 | 13 |
Chains H and S: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-10 | 5 | 13 |
| β-strand | 14 | 1 | 15 |
| β-strand | 21 | 1 | 13 |
| β-strand | 24 | 1 | 15 |
| β-strand | 29-32 | 4 | 13 |
| α-helix | 34-36 | 3 | |
| β-strand | 39-43 | 5 | 13 |
| β-strand | 49-53 | 5 | 13 |
| α-helix | 54-56 | 3 | |
| β-strand | 57-59 | 3 | 13 |
Chain I: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-10 | 6 | 16 |
| β-strand | 14 | 1 | 17 |
| β-strand | 21 | 1 | 16 |
| β-strand | 24 | 1 | 17 |
| β-strand | 29-33 | 5 | 16 |
| β-strand | 39-43 | 5 | 16 |
| β-strand | 49-53 | 5 | 16 |
| α-helix | 54-56 | 3 | |
| β-strand | 57 | 1 | 18 |
15 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cytoplasmic protein NCK1 | 1, 2, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z | protein | 87 | Homo sapiens | P16333 (AlphaFold model) |
Sequence of entity 1 (1, 2, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z), FASTA
>5QU6_1 Cytoplasmic protein NCK1 (chains 1, 2, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z)
SGGLNDIFEAQKIEWHEGSENLYFQSMAEEVVVVAKFDYVAQQEQELDIKKNERLWLLDD
SKSWWRVRNSMNKTGFVPSNYVERKNS
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
- 5QU2 1.04 Å, Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY
- 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
- 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
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