Research workbench
Structure of HIV cleaved synaptic complex (csc) intasome bound with magnesium and insti XZ426 (compound 4D)
Analyse Structure of HIV cleaved synaptic complex (csc) intasome bound with magnesium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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