Research workbench
Crystal structure of the S. pombe peptidase homology domain of fact complex subunit SPT16 (form a)
Analyse Crystal structure of the S. pombe peptidase homology domain of fact complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CB5
- Type
- protein
- Length
- 884 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fact complex subunit SPT16
- UniProt
- O94267
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fact complex subunit SPT16 | protein | 444 | 41% helix, 22% strand | O94267 |
| B | Fact complex subunit SPT16 | protein | 440 | 40% helix, 21% strand | O94267 |
Ligands and binding sites
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.75 | 0.78 | 119 | empty |
| 2 | 338 | 0.61 | 0.78 | 61 | empty |
| 3 | 198 | 0.58 | 0.80 | 36 | empty |
| 4 | 152 | 0.50 | 0.78 | 18 | empty |
| 5 | 113 | 0.48 | 0.80 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 819 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3CB5 · Crystal Structure of the S. pombe Peptidase Homology Domain of FACT complex subunit Spt16… · the same entry in another collection · chain A against A, TM-score 1.00
- O94267 · AlphaFold monomer V2.0 prediction for fact complex subunit SPT16 (O94267) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O94267
- Elsewhere: RCSB PDB 3CB5 · PDBe 3CB5 · UniProt O94267
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