MolNFT v1 · #127089 · protein + DNA
Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ379 (compound 5'G)
5MMA · Integrase: “Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ379…”. X-ray diffraction, 4 ligands (VHT, MG, ZN), 9 pockets (best druggability 0.70). MolNFT v1 #127089 on…
- PDB
- 5MMA
- 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
- VHT, MG, ZN, SO4
- 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 | 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 | 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, 18% 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
- VHT · methyl 2-[[3-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridin-4-yl]amino]ethanoate · 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 · 5 copies · chains A, D, B
- GOL · Glycerol · additive · 12 copies · chains A, C, D, B
- HEZ · Hexane-1,6-diol · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
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 | 556 | 0.70 | 0.79 | 41 | HEZ |
| 2 | 328 | 0.68 | 0.82 | 48 | GOL |
| 3 | 188 | 0.51 | 0.77 | 25 | SO4 |
| 4 | 71 | 0.50 | 0.84 | 15 | HEZ |
| 5 | 105 | 0.47 | 0.80 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1437 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1139 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 735 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- A–D · 305 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5MMA · 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 5MMA · PDBe 5MMA · UniProt P14350
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