Research workbench
PFV target capture complex (TCC) at 3.32 A resolution
Analyse PFV target capture complex (TCC) at 3.32 A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OS2
- Type
- protein + DNA
- Length
- 580 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.32
- Source
- Human spumaretrovirus; SYNTHETIC CONSTRUCT
- Molecule
- Integrase; DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3'); DNA…
- UniProt
- P14350
- Ligands
- ZN, SO4
- Pockets
- 13 · best druggability 0.63
Structure
x-ray diffraction · resolution 3.32 · 5 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 365 | 31% helix, 20% strand | P14350 |
| B | Integrase | protein | 163 | 38% helix, 18% strand | P14350 |
| C | DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3') | dna | 19 | — | — |
| D | DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3') | dna | 17 | — | — |
| T | DNA (5'-D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*CP*TP*CP*GP*GP*G)-3') | dna | 16 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.63 | 0.77 | 36 | empty |
| 2 | 72 | 0.56 | 0.88 | 25 | empty |
| 3 | 248 | 0.55 | 0.78 | 40 | empty |
| 4 | 72 | 0.51 | 0.85 | 21 | empty |
| 5 | 87 | 0.49 | 0.83 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1399 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1182 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–D · 748 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- A–T · 500 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 356 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 3OS2 · Pfv target capture complex (tcc) at 3.32 a resolution · 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 P14350
- Elsewhere: RCSB PDB 3OS2 · PDBe 3OS2 · UniProt P14350
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