MolNFT v1 · #69851 · protein + DNA
Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium
3L2R · Integrase: “Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium”. X-ray diffraction, 3 ligands (MG, ZN, NH4), 8 pockets (best druggability 0.68). MolNFT v1 #69851 on GenesisL1: 3D structure…
- PDB
- 3L2R
- Type
- protein + DNA
- Length
- 564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; 5'- D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A) -3'; 5'…
- UniProt
- P14350
- Ligands
- MG, ZN, NH4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 365 | 34% helix, 22% strand | P14350 |
| B | Integrase | protein | 163 | 37% helix, 18% strand | P14350 |
| C | 5'- D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A) -3' | dna | 19 | — | — |
| D | 5'- D(*TP*AP*CP*AP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3' | dna | 17 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D, B
- ZN · Zinc ion · metal · chains A
- NH4 · Ammonium ion · ion · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.68 | 0.78 | 52 | empty |
| 2 | 395 | 0.68 | 0.81 | 55 | empty |
| 3 | 53 | 0.58 | 0.91 | 20 | empty |
| 4 | 66 | 0.48 | 0.84 | 15 | empty |
| 5 | 77 | 0.43 | 0.80 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1415 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1144 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 730 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–D · 357 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 3L2R · 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 3L2R · PDBe 3L2R · UniProt P14350
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