MolNFT v1 · #172799 · protein + DNA
Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ447 (compound 6V)
7ADV · Integrase: “Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ447…”. X-ray diffraction, 4 ligands (R7N, MG, ZN), 7 pockets (best druggability 0.70). MolNFT v1 #172799 on…
- PDB
- 7ADV
- Type
- protein + DNA
- Length
- 585 residues
- Chains
- 4
- 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…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-
- UniProt
- P14350
- Ligands
- R7N, MG, ZN, SO4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-) | protein | 367 | 32% helix, 21% strand | P14350 |
| B | Integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-) | protein | 182 | 36% helix, 16% 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 | — | — |
Ligands and binding sites
- R7N · 4-azanyl-~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-6-[2-(2-morpholin-4-ylethylsulfonyl)ethyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide · ligand · chains A, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, D, B
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 17 copies · chains A, C, D, B
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.70 | 0.78 | 45 | SO4 |
| 2 | 307 | 0.65 | 0.81 | 45 | SO4, GOL |
| 3 | 194 | 0.49 | 0.76 | 21 | MG, R7N, SO4 |
| 4 | 69 | 0.49 | 0.84 | 16 | SO4 |
| 5 | 83 | 0.42 | 0.80 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1458 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1162 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–D · 735 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- A–D · 313 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 7ADV · Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium… · 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 7ADV · PDBe 7ADV · UniProt P14350
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