MolNFT v1 · #74278 · protein + DNA
Pfv target capture complex (tcc) at 2.97 a resolution
3OS1 · Integrase: “Pfv target capture complex (tcc) at 2.97 a resolution”. X-ray diffraction, 3 ligands (MG, ZN, SO4), 10 pockets (best druggability 0.68). MolNFT v1 #74278 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OS1
- Type
- protein + DNA
- Length
- 580 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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
- MG, ZN, SO4
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 365 | 33% helix, 20% strand | P14350 |
| B | Integrase | protein | 163 | 40% 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*(2DA))-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
- MG · Magnesium ion · metal · 2 copies · chains B, A, D, T
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.68 | 0.82 | 56 | empty |
| 2 | 505 | 0.65 | 0.76 | 50 | empty |
| 3 | 90 | 0.51 | 0.83 | 15 | empty |
| 4 | 62 | 0.45 | 0.83 | 16 | empty |
| 5 | 125 | 0.44 | 0.77 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1410 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1165 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 742 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- A–T · 507 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 361 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3OS1 · PFV target capture complex (TCC) at 2.97 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 3OS1 · PDBe 3OS1 · UniProt P14350
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