MolNFT v1 · #184569 · protein + DNA
Stlv-1 INTASOME:B56 in complex with the strand-transfer inhibitor raltegravir
7OUG · Integrase: “Stlv-1 INTASOME:B56 in complex with the strand-transfer inhibitor raltegravir”. Electron microscopy, 3 ligands (RLT, ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1 #184569 on GenesisL1: 3D structure, binding…
- PDB
- 7OUG
- Type
- protein + DNA
- Length
- 1,744 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; Isoform 3 of PC4 and SFRS1-interacting PROTEIN,ISOFORM gamma-2 of…
- UniProt
- Q4QY51, Q13362
- Ligands
- RLT, ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Integrase | protein | 258 | 33% helix, 22% strand | Q4QY51 |
| E, B | Integrase | protein | 278 | 36% helix, 21% strand | Q4QY51 |
| F, C | 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 | 65% helix, 0% strand | Q13362 |
| 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
- RLT · N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl) carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.85 | 0.88 | 87 | empty |
| 2 | 834 | 0.84 | 0.87 | 91 | empty |
| 3 | 1190 | 0.81 | 0.82 | 118 | empty |
| 4 | 1112 | 0.79 | 0.80 | 93 | empty |
| 5 | 361 | 0.71 | 0.83 | 42 | empty |
Interfaces
27 interfaces between chains.
- A–B · 1721 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 1711 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1509 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1506 Ų buried · 9 hydrogen bonds · protein-protein
- E–B · 1233 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7OUG · STLV-1 intasome:B56 in complex with the strand-transfer inhibitor raltegravir · the same entry in another collection · chain L against L, 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 F 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 7OUG · PDBe 7OUG · UniProt Q4QY51 · UniProt Q13362
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