Research workbench
Pfv intasome prior to 3'-processing, apo form (ui-apo)
Analyse Pfv intasome prior to 3'-processing, apo form (ui-apo) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E7H
- Type
- protein + DNA
- Length
- 590 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pro-pol polyprotein; DNA (5'- D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-
- UniProt
- P14350
- Ligands
- ZN, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pro-pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-) | protein | 368 | 34% helix, 21% strand | P14350 |
| B | Pro-pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-) | protein | 184 | 39% 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*AP*AP*T)-3') | dna | 19 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- GOL · Glycerol · additive · 9 copies · chains A, C, D, B
- HEZ · Hexane-1,6-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.70 | 0.77 | 50 | SO4 |
| 2 | 388 | 0.68 | 0.81 | 54 | SO4, GOL |
| 3 | 75 | 0.51 | 0.84 | 15 | empty |
| 4 | 199 | 0.51 | 0.76 | 25 | SO4 |
| 5 | 98 | 0.46 | 0.80 | 19 | GOL |
Interfaces
4 interfaces between chains.
- A–B · 1426 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1134 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–D · 743 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–D · 638 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 4E7H · PFV intasome prior to 3'-processing, Apo form (UI-Apo) · 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 4E7H · PDBe 4E7H · UniProt P14350
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