MolNFT v1 · #78257 · protein + DNA
Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and dolutegravir (S/GSK1349572)
3S3M · Pfv integrase: “Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and dolutegravir…”. X-ray diffraction, 5 ligands (DLU, MG, ZN), 11 pockets (best druggability 0.68). MolNFT v1 #78257 on…
- PDB
- 3S3M
- Type
- protein + DNA
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pfv integrase; 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP *a)-3'…
- EC
- 2.7.7.-
- UniProt
- P14350
- Ligands
- DLU, MG, ZN, SO4, NH4
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfv integrase (EC 2.7.7.-) | protein | 368 | 34% helix, 21% strand | P14350 |
| B | Pfv integrase (EC 2.7.7.-) | protein | 184 | 38% helix, 17% strand | P14350 |
| C | 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 | 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
- DLU · (4r,12as)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6, 8-dioxo-3,4,6,8,12,12A-hexahydro-2H-pyrido[1',2':4, 5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide · ligand · chains A, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- 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
- HEZ · Hexane-1,6-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.68 | 0.78 | 40 | HEZ |
| 2 | 90 | 0.62 | 0.89 | 24 | empty |
| 3 | 255 | 0.56 | 0.78 | 28 | empty |
| 4 | 286 | 0.53 | 0.75 | 33 | MG, DLU |
| 5 | 237 | 0.53 | 0.76 | 39 | GOL, SO4 |
Interfaces
4 interfaces between chains.
- A–B · 1448 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1153 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–D · 730 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- A–D · 307 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 3S3M · 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 3S3M · PDBe 3S3M · UniProt P14350
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