MolNFT v1 · #90049 · protein + DNA
Pfv integrase target capture complex, apo form (tcc-apo), at 3.15 a resolution
4E7J · Pro-pol polyprotein: “Pfv integrase target capture complex, apo form (tcc-apo), at 3.15 a resolution”. X-ray diffraction, 2 ligands (ZN, SO4), 9 pockets (best druggability 0.67). MolNFT v1 #90049 on GenesisL1: 3D structure, binding…
- PDB
- 4E7J
- Type
- protein + DNA
- Length
- 579 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
- ZN, SO4
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 19% 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 | 365 | 31% helix, 20% strand | P14350 |
| B | Pro-pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-) | protein | 163 | 36% helix, 17% 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 | 15 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.67 | 0.82 | 53 | empty |
| 2 | 496 | 0.66 | 0.77 | 44 | empty |
| 3 | 62 | 0.48 | 0.85 | 15 | empty |
| 4 | 106 | 0.43 | 0.78 | 22 | empty |
| 5 | 51 | 0.38 | 0.81 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1406 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1162 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–D · 744 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- A–T · 501 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 364 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4E7J · PFV integrase Target Capture Complex, Apo form (TCC-Apo), at 3.15 A resolution · 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 4E7J · PDBe 4E7J · UniProt P14350
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