MolNFT v1 · #74491 · protein + DNA
Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti MK2048
3OYB · Pfv integrase: “Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti MK2048”. X-ray diffraction, 5 ligands (ZZX, MG, ZN), 9 pockets (best druggability 0.70). MolNFT v1 #74491 on…
- PDB
- 3OYB
- Type
- protein + DNA
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pfv integrase; DNA (5'- D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')…
- UniProt
- P14350
- Ligands
- ZZX, MG, ZN, SO4, NH4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfv integrase | protein | 368 | 34% helix, 21% strand | P14350 |
| B | Pfv integrase | protein | 184 | 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
- ZZX · (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N, 6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1', 2':1,5]pyrrolo[2,3-d]pyridazine-4-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 · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.70 | 0.82 | 57 | empty |
| 2 | 525 | 0.69 | 0.78 | 40 | empty |
| 3 | 199 | 0.49 | 0.76 | 22 | MG, ZZX |
| 4 | 175 | 0.49 | 0.77 | 30 | SO4 |
| 5 | 67 | 0.47 | 0.83 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1433 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1145 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–D · 733 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–D · 299 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 3OYB · Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium… · the same entry in another collection · chain B against B, 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 3OYB · PDBe 3OYB · UniProt P14350
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