MolNFT v1 · #171064 · protein
Structure of the homo sapiens sas-6 coiled-coil domain
6YS4 · Spindle assembly abnormal protein 6 homolog: “Structure of the homo sapiens sas-6 coiled-coil domain”. X-ray diffraction, 1 ligand (GLY), 7 pockets (best druggability 0.69). MolNFT v1 #171064 on GenesisL1: 3D structure, binding…
- PDB
- 6YS4
- Type
- protein
- Length
- 591 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindle assembly abnormal protein 6 homolog
- UniProt
- Q6UVJ0
- Ligands
- GLY
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 98% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Spindle assembly abnormal protein 6 homolog | protein | 103 | 98% helix, 0% strand | Q6UVJ0 |
| B | Spindle assembly abnormal protein 6 homolog | protein | 102 | 98% helix, 0% strand | Q6UVJ0 |
| C | Spindle assembly abnormal protein 6 homolog | protein | 95 | 97% helix, 0% strand | Q6UVJ0 |
| D | Spindle assembly abnormal protein 6 homolog | protein | 87 | 97% helix, 0% strand | Q6UVJ0 |
| F | Spindle assembly abnormal protein 6 homolog | protein | 101 | 98% helix, 0% strand | Q6UVJ0 |
Ligands and binding sites
- GLY · Glycine · ligand · 3 copies · chains C, B, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.69 | 0.78 | 51 | GLY |
| 2 | 531 | 0.63 | 0.75 | 42 | empty |
| 3 | 396 | 0.63 | 0.78 | 38 | empty |
| 4 | 305 | 0.61 | 0.79 | 43 | empty |
| 5 | 140 | 0.56 | 0.82 | 26 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2539 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2520 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2377 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 568 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 552 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 6YS4 · Structure of the Homo sapiens SAS-6 coiled-coil domain · the same entry in another collection · chain F against F, TM-score 1.00
- Q6UVJ0 · AlphaFold monomer V2.0 prediction for spindle assembly abnormal protein 6 homolog (Q6UVJ0) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q6UVJ0
- Elsewhere: RCSB PDB 6YS4 · PDBe 6YS4 · UniProt Q6UVJ0
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