Research workbench
Structure of the stlv INTASOME:B56 complex bound to the strand- transfer inhibitor bictegravir
Analyse Structure of the stlv INTASOME:B56 complex bound to the strand- transfer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OUH
- Type
- protein + DNA
- Length
- 1,744 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; PC4 and SFRS1-interacting PROTEIN,SERINE/THREONINE-protein phosphatase 2A 56…
- UniProt
- Q4QY51
- Ligands
- KLQ, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Integrase | protein | 258 | 33% helix, 21% strand | Q4QY51 |
| E, B | Integrase | protein | 278 | 35% helix, 21% strand | Q4QY51 |
| F, C | PC4 and SFRS1-interacting PROTEIN,SERINE/THREONINE-protein phosphatase 2A 56 kda regulatory subunit gamma isoform | protein | 296 | 63% helix, 0% strand | — |
| I, K | 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 | — | — |
| J, L | 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
- KLQ · Bictegravir · ligand · 2 copies · chains E, I, J, B, K, L
- ZN · Zinc ion · metal · 4 copies · chains D, E, A, B
- MG · Magnesium ion · metal · 4 copies · chains E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.84 | 0.85 | 102 | empty |
| 2 | 906 | 0.83 | 0.85 | 86 | empty |
| 3 | 893 | 0.82 | 0.84 | 109 | empty |
| 4 | 1160 | 0.80 | 0.82 | 114 | empty |
| 5 | 145 | 0.74 | 0.92 | 41 | empty |
Interfaces
27 interfaces between chains.
- A–B · 1732 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1727 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1610 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1610 Ų buried · 14 hydrogen bonds · protein-protein
- E–B · 1269 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7OUH · Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor… · the same entry in another collection · chain C against C, 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 Q4QY51
- Elsewhere: RCSB PDB 7OUH · PDBe 7OUH · UniProt Q4QY51
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