MolNFT v1 · #90051 · protein + DNA
Pfv integrase strand transfer complex (stc-mn*) following reaction in crystallo, at 3.0 a resolution.
4E7L · Pro-pol polyprotein: “Pfv integrase strand transfer complex (stc-mn*) following reaction in crystallo, at 3.0 a resolution.”. X-ray diffraction, 3 ligands (MN, ZN, SO4), 12 pockets (best druggability 0.64). MolNFT v1 #90051 on…
- PDB
- 4E7L
- Type
- protein + DNA
- Length
- 580 residues
- Chains
- 6
- 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
- 12 · best druggability 0.64
Structure
x-ray diffraction · 6 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 | 365 | 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 | 40% 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 | — | — |
| t | DNA (5'-D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*G)-3') | dna | 6 | — | — |
| T | DNA (5'- D(P*CP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*CP*TP*CP*GP*GP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, D, t, T, B
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.64 | 0.80 | 50 | empty |
| 2 | 414 | 0.62 | 0.77 | 38 | empty |
| 3 | 82 | 0.50 | 0.83 | 14 | MN |
| 4 | 63 | 0.43 | 0.82 | 15 | empty |
| 5 | 104 | 0.41 | 0.77 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1419 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1156 Ų buried · 28 hydrogen bonds · protein-nucleic
- C–D · 745 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–D · 353 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–t · 345 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4E7L · PFV integrase Strand Transfer Complex (STC-Mn*) following reaction in crystallo, at 3.0 A… · 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 4E7L · PDBe 4E7L · UniProt P14350
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.