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Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ434 (compound 6P)
Analyse Crystal structure of the prototype foamy virus (pfv) intasome in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MMB
- Type
- protein + DNA
- Length
- 585 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')…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-
- UniProt
- P14350
- Ligands
- OUY, MG, ZN, SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfv integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-) | protein | 367 | 34% helix, 21% strand | P14350 |
| B | Pfv integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-) | protein | 182 | 38% 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
- OUY · Methyl 3-[5-azanyl-6-[[2,4-bis(fluoranyl) phenyl]methylcarbamoyl]-8-oxidanyl-7-oxidanylidene-1, 8-naphthyridin-3-yl]propanoate · 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 · 9 copies · chains A, D, B, C
- GOL · Glycerol · additive · 7 copies · chains A, C, B, D
- HEZ · Hexane-1,6-diol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.71 | 0.78 | 48 | SO4, HEZ |
| 2 | 373 | 0.68 | 0.81 | 45 | SO4, GOL |
| 3 | 212 | 0.51 | 0.77 | 25 | MG, OUY |
| 4 | 192 | 0.50 | 0.76 | 26 | SO4 |
| 5 | 68 | 0.50 | 0.85 | 15 | HEZ |
Interfaces
4 interfaces between chains.
- A–B · 1458 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1149 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–D · 730 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–D · 315 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5MMB · Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium… · the same entry in another collection · chain D against D, 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 5MMB · PDBe 5MMB · UniProt P14350
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