Research workbench
Crystal structure of swapped human nck SH3.1 domain, 1.05A, orthorhombic form I
Analyse Crystal structure of swapped human nck SH3.1 domain, 1.05A, orthorhombic form I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QU4
- Type
- protein
- Length
- 228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytoplasmic protein NCK1
- UniProt
- P16333
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytoplasmic protein NCK1 | protein | 57 | 5% helix, 56% strand | P16333 |
| B | Cytoplasmic protein NCK1 | protein | 62 | 10% helix, 42% strand | P16333 |
| C | Cytoplasmic protein NCK1 | protein | 55 | 5% helix, 40% strand | P16333 |
| D | Cytoplasmic protein NCK1 | protein | 54 | 6% helix, 39% strand | P16333 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.33 | 0.75 | 11 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2309 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2194 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 181 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 168 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 110 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5QU4 · Crystal Structure of swapped human Nck SH3.1 domain, 1.05A, orthorhombic form I · the same entry in another collection · chain D against D, TM-score 1.00
- P16333 · AlphaFold monomer V2.0 prediction for cytoplasmic protein NCK1 (P16333) · a predicted model of the same protein · chain A against A, TM-score 0.57
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 P16333
- Elsewhere: RCSB PDB 5QU4 · PDBe 5QU4 · UniProt P16333
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