Research workbench
Prototype foamy virus strand transfer complexes on product DNA
Analyse Prototype foamy virus strand transfer complexes on product DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BAC
- Type
- protein + DNA
- Length
- 616 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*TP*GP*TP*AP)-3'; DNA…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P14350
- Ligands
- MG, ZN
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 368 | 32% helix, 20% strand | P14350 |
| B | Integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 184 | 35% helix, 16% strand | P14350 |
| C | 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*TP*GP*TP*AP)-3' | dna | 19 | — | — |
| D | DNA (38-mer) | dna | 33 | — | — |
| E | 5'-D(*AP*GP*GP*AP*GP*CP*CP*AP*AP*GP*AP*CP*GP*GP *AP*TP*CP)- 3' | dna | 12 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.68 | 0.93 | 26 | empty |
| 2 | 517 | 0.67 | 0.78 | 42 | empty |
| 3 | 191 | 0.55 | 0.79 | 29 | empty |
| 4 | 214 | 0.49 | 0.75 | 23 | empty |
| 5 | 170 | 0.49 | 0.77 | 25 | MG |
Interfaces
5 interfaces between chains.
- A–B · 1529 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1198 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–D · 738 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- D–E · 564 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–D · 490 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 4BAC · prototype foamy virus strand transfer complexes on product DNA · 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 4BAC · PDBe 4BAC · UniProt P14350
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