Research workbench
Pfv integrase target capture complex (tcc-mn), freeze-trapped prior to strand transfer, at 3.0 a resolution
Analyse Pfv integrase target capture complex (tcc-mn), freeze-trapped prior to strand… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E7K
- Type
- protein + DNA
- Length
- 583 residues
- Chains
- 5
- 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
- MN, ZN, SO4
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 21% 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 | 366 | 33% 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 | 163 | 39% helix, 19% 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 | — | — |
| T | DNA (5'- D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*GP*CP*AP*CP*GP*TP* GP*CP*CP*TP*CP*GP*GP*G)-3') | dna | 18 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, D, T, B
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains B
- PGE · Triethylene glycol · additive · chains T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.73 | 0.83 | 61 | empty |
| 2 | 461 | 0.65 | 0.77 | 40 | empty |
| 3 | 103 | 0.50 | 0.82 | 16 | empty |
| 4 | 58 | 0.50 | 0.86 | 14 | empty |
| 5 | 115 | 0.47 | 0.79 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1400 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1124 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–D · 733 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- A–T · 478 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 364 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 4E7K · PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer… · 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 4E7K · PDBe 4E7K · UniProt P14350
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