Research workbench
SF3B10-SF3B130 from chaetomium thermophilum
Analyse SF3B10-SF3B130 from chaetomium thermophilum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HY7
- Type
- protein
- Length
- 2,453 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pre-mRNA splicing protein; YSF3
- UniProt
- G0S5A2, G0S133
- Ligands
- CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative pre-mRNA splicing protein | protein | 1173 | 6% helix, 49% strand | G0S5A2 |
| D, C | YSF3 | protein | 55 | 71% helix, 0% strand | G0S133 |
| B | Putative pre-mRNA splicing protein | protein | 1170 | 8% helix, 48% strand | G0S5A2 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.84 | 0.85 | 62 | empty |
| 2 | 1185 | 0.84 | 0.85 | 90 | CA |
| 3 | 1193 | 0.84 | 0.85 | 65 | empty |
| 4 | 1128 | 0.84 | 0.84 | 101 | CA |
| 5 | 974 | 0.79 | 0.81 | 81 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2033 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 2011 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 574 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5HY7 · SF3B10-SF3B130 from Chaetomium thermophilum · the same entry in another collection · chain A against A, TM-score 1.00
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 G0S5A2
- Every structure of UniProt G0S133
- Elsewhere: RCSB PDB 5HY7 · PDBe 5HY7 · UniProt G0S5A2 · UniProt G0S133
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