MolNFT v1 · #136240 · protein
Crystal structure of the middle double pH domain of human fact complex subunit SPT16
5UMU: “Crystal structure of the middle double pH domain of human fact complex subunit SPT16”. X-ray diffraction, 3 pockets (best druggability 0.74). MolNFT v1 #136240 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UMU
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fact complex subunit SPT16
- UniProt
- Q9Y5B9
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fact complex subunit SPT16 | protein | 258 | 25% helix, 39% strand | Q9Y5B9 |
| B | Fact complex subunit SPT16 | protein | 258 | 26% helix, 39% strand | Q9Y5B9 |
Ligands and binding sites
- FMT · Formic acid · additive · 25 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.74 | 0.78 | 83 | FMT |
| 2 | 121 | 0.40 | 0.75 | 19 | FMT |
| 3 | 75 | 0.30 | 0.73 | 19 | FMT |
Interfaces
1 interface between chains.
- A–B · 554 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 5UMU · Crystal structure of the middle double PH domain of human FACT complex subunit SPT16 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5B9 · AlphaFold monomer V2.0 prediction for fact complex subunit SPT16 (Q9Y5B9) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9Y5B9
- Elsewhere: RCSB PDB 5UMU · PDBe 5UMU · UniProt Q9Y5B9
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