Research workbench
Cryoem structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma
Analyse Cryoem structure of simian T-cell lymphotropic virus intasome in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PEL
- Type
- protein + DNA
- Length
- 1,744 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol protein; Isoform 3 of PC4 and SFRS1-interacting PROTEIN,ISOFORM gamma-2 of…
- UniProt
- Q4QY51, Q13362
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pol protein | protein | 258 | 33% helix, 22% strand | Q4QY51 |
| B, E | Pol protein | protein | 278 | 33% helix, 20% strand | Q4QY51 |
| C, F | Isoform 3 of PC4 and SFRS1-interacting PROTEIN,ISOFORM gamma-2 of SERINE/THREONINE-protein phosphatase 2A 56 kda regulatory subunit gamma isoform | protein | 296 | 58% helix, 0% strand | Q13362 |
| K, M | DNA (5'- D(*AP*CP*TP*GP*TP*GP*TP*TP*TP*GP*GP*CP*GP*CP*TP*TP*CP*TP*CP*TP*C)- 3') | dna | 21 | — | — |
| L, N | DNA (5'- D(*GP*AP*GP*AP*GP*AP*AP*GP*CP*GP*CP*CP*AP*AP*AP*CP*AP*CP*A)-3') | dna | 19 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.84 | 0.85 | 105 | empty |
| 2 | 869 | 0.83 | 0.85 | 81 | empty |
| 3 | 921 | 0.79 | 0.82 | 85 | empty |
| 4 | 619 | 0.78 | 0.84 | 69 | empty |
| 5 | 357 | 0.72 | 0.84 | 39 | empty |
Interfaces
27 interfaces between chains.
- A–B · 1729 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1726 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1512 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1504 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 1275 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7PEL · CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A… · the same entry in another collection · chain N against N, TM-score 1.00
- Q13362 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2A 56 kda… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q4QY51
- Every structure of UniProt Q13362
- Elsewhere: RCSB PDB 7PEL · PDBe 7PEL · UniProt Q4QY51 · UniProt Q13362
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