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The crystal structure of an archaeal cpsf subunit, PH1404 from pyrococcus horikoshii complexed with RNA-analog
Analyse The crystal structure of an archaeal cpsf subunit, PH1404 from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AF6
- Type
- protein + RNA
- Length
- 641 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein PH1404; 5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3…
- UniProt
- O50112
- Ligands
- ZN, SO4, SSU
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein PH1404 | protein | 637 | 33% helix, 21% strand | O50112 |
| B | 5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3' | rna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- SSU · Uridine-5'-phosphorothioate · ion · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.78 | 0.80 | 89 | empty |
| 2 | 227 | 0.75 | 0.90 | 42 | SO4 |
| 3 | 347 | 0.61 | 0.78 | 39 | empty |
| 4 | 125 | 0.40 | 0.75 | 25 | empty |
| 5 | 87 | 0.38 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 647 Ų buried · 26 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 3AF6 · The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii… · 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 O50112
- Elsewhere: RCSB PDB 3AF6 · PDBe 3AF6 · UniProt O50112
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