Research workbench
Pandda analysis group deposition -- crystal structure of human STAG1 in complex with Z2856434884
Analyse Pandda analysis group deposition -- crystal structure of human STAG1 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QSW
- Type
- protein
- Length
- 1,221 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cohesin subunit sa-1
- UniProt
- Q8WVM7
- Ligands
- O3J
- Pockets
- 11 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cohesin subunit sa-1 | protein | 315 | 78% helix, 0% strand | Q8WVM7 |
| A | Cohesin subunit sa-1 | protein | 297 | 75% helix, 0% strand | Q8WVM7 |
| B | Cohesin subunit sa-1 | protein | 298 | 78% helix, 0% strand | Q8WVM7 |
| D | Cohesin subunit sa-1 | protein | 311 | 78% helix, 0% strand | Q8WVM7 |
Ligands and binding sites
- O3J · 1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one · ligand · 4 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.59 | 0.86 | 16 | O3J |
| 2 | 104 | 0.54 | 0.83 | 18 | O3J |
| 3 | 97 | 0.50 | 0.82 | 17 | O3J |
| 4 | 67 | 0.48 | 0.84 | 15 | O3J |
| 5 | 107 | 0.35 | 0.73 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1108 Ų buried · 4 hydrogen bonds · protein-protein
- C–A · 1093 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 677 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 647 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5QSW · PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8WVM7 · AlphaFold monomer V2.0 prediction for cohesin subunit sa-1 (Q8WVM7) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q8WVM7
- Elsewhere: RCSB PDB 5QSW · PDBe 5QSW · UniProt Q8WVM7
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