Research workbench
Mouse mammary tumor virus strand transfer complex intasome
Analyse Mouse mammary tumor virus strand transfer complex intasome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7USF
- Type
- protein + DNA
- Length
- 1,068 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; Vdna strand (non-transferred); Vdna-tdna strand (transferred); Tdna strand
- UniProt
- O56220
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 7 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 265 | 41% helix, 20% strand | O56220 |
| B | Integrase | protein | 252 | 38% helix, 20% strand | O56220 |
| C | Integrase | protein | 240 | 42% helix, 23% strand | O56220 |
| D | Integrase | protein | 235 | 41% helix, 23% strand | O56220 |
| I | Vdna strand (non-transferred) | dna | 22 | — | — |
| J | Vdna-tdna strand (transferred) | dna | 40 | — | — |
| K | Tdna strand | dna | 14 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.77 | 0.80 | 52 | empty |
| 2 | 317 | 0.75 | 0.87 | 35 | empty |
| 3 | 879 | 0.72 | 0.77 | 73 | empty |
| 4 | 276 | 0.69 | 0.84 | 33 | empty |
| 5 | 214 | 0.56 | 0.78 | 25 | empty |
Interfaces
9 interfaces between chains.
- C–D · 2229 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2028 Ų buried · 11 hydrogen bonds · protein-protein
- A–I · 944 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 899 Ų buried · 4 hydrogen bonds · protein-protein
- I–J · 878 Ų buried · 71 hydrogen bonds · nucleic-nucleic
Compared structures
- 7USF · Mouse mammary tumor virus strand transfer complex intasome · 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 O56220
- Elsewhere: RCSB PDB 7USF · PDBe 7USF · UniProt O56220
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