MolNFT v1 · #160805 · protein + DNA
Structure of HIV cleaved synaptic complex (csc) intasome bound with magnesium and insti XZ426 (compound 4D)
6PUY · Chimeric SSO7D and HIV-1 integrase: “Structure of HIV cleaved synaptic complex (csc) intasome bound with magnesium and insti XZ426 (compound 4D)”. Electron microscopy, 3 ligands (OZ1, MG, ZN), 8 pockets (best druggability 0.72).…
- PDB
- 6PUY
- Type
- protein + DNA
- Length
- 652 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimeric SSO7D and HIV-1 integrase; Viral DNA non-transferred strand; Viral DNA…
- UniProt
- P39476, Q76353
- Ligands
- OZ1, MG, ZN
- Pockets
- 8 · best druggability 0.72
Structure
electron microscopy · 6 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimeric SSO7D and HIV-1 integrase | protein | 261 | 45% helix, 22% strand | P39476, Q76353 |
| B | Chimeric SSO7D and HIV-1 integrase | protein | 242 | 45% helix, 25% strand | P39476, Q76353 |
| C | Chimeric SSO7D and HIV-1 integrase | protein | 66 | 15% helix, 39% strand | P39476, Q76353 |
| D | Chimeric SSO7D and HIV-1 integrase | protein | 47 | 6% helix, 60% strand | P39476, Q76353 |
| E | Viral DNA non-transferred strand | dna | 19 | — | — |
| F | Viral DNA transferred strand | dna | 17 | — | — |
Ligands and binding sites
- OZ1 · 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide · ligand · chains A, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, F
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.72 | 0.76 | 86 | empty |
| 2 | 317 | 0.59 | 0.77 | 37 | empty |
| 3 | 325 | 0.57 | 0.76 | 43 | empty |
| 4 | 102 | 0.49 | 0.81 | 20 | empty |
| 5 | 111 | 0.43 | 0.76 | 15 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1636 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1635 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 821 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 748 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 712 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Compared structures
- 6PUY · Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI… · the same entry in another collection · chain F against F, TM-score 1.00
- P39476 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P39476) · a predicted model of the same protein · chain D against A, TM-score 0.50
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 P39476
- Every structure of UniProt Q76353
- Elsewhere: RCSB PDB 6PUY · PDBe 6PUY · UniProt P39476 · UniProt Q76353
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