Research workbench
Structure of the PDS5-SCC1 complex and implications for cohesin function
Analyse Structure of the PDS5-SCC1 complex and implications for cohesin function in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FRP
- Type
- protein
- Length
- 1,371 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sister chromatid cohesion protein PDS5; MCD1-like protein
- UniProt
- Q04264, Q12158
- Pockets
- 18 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sister chromatid cohesion protein PDS5 | protein | 677 | 70% helix, 0% strand | Q04264 |
| B | Sister chromatid cohesion protein PDS5 | protein | 660 | 71% helix, 0% strand | Q04264 |
| C, D | MCD1-like protein | protein | 17 | 0% helix, 6% strand | Q12158 |
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.73 | 0.84 | 50 | empty |
| 2 | 392 | 0.71 | 0.82 | 55 | empty |
| 3 | 317 | 0.67 | 0.82 | 49 | empty |
| 4 | 360 | 0.66 | 0.80 | 46 | empty |
| 5 | 82 | 0.65 | 0.90 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2460 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 895 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 894 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 92 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 91 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5FRP · Structure of the Pds5-Scc1 complex and implications for cohesin function · the same entry in another collection · chain A against A, TM-score 1.00
- Q04264 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein PDS5 (Q04264) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q12158 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein 1 (Q12158) · a predicted model of the same protein · chain C against A, TM-score 0.25
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 Q04264
- Every structure of UniProt Q12158
- Elsewhere: RCSB PDB 5FRP · PDBe 5FRP · UniProt Q04264 · UniProt Q12158
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