MolNFT v1 · #160806 · protein + DNA
Structure of HIV cleaved synaptic complex (csc) intasome bound with magnesium and insti XZ446 (compound 4F)
6PUZ · Chimeric SSO7D and HIV-1 integrase: “Structure of HIV cleaved synaptic complex (csc) intasome bound with magnesium and insti XZ446 (compound 4F)”. Electron microscopy, 3 ligands (XXJ, MG, ZN), 11 pockets (best druggability 0.67).…
- PDB
- 6PUZ
- Type
- protein + DNA
- Length
- 651 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
- XXJ, MG, ZN
- Pockets
- 11 · best druggability 0.67
Structure
electron microscopy · 6 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimeric SSO7D and HIV-1 integrase | protein | 262 | 43% helix, 18% strand | P39476, Q76353 |
| B | Chimeric SSO7D and HIV-1 integrase | protein | 240 | 44% helix, 25% strand | P39476, Q76353 |
| C | Chimeric SSO7D and HIV-1 integrase | protein | 65 | 15% helix, 45% strand | P39476, Q76353 |
| D | Chimeric SSO7D and HIV-1 integrase | protein | 48 | 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
- XXJ · 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.67 | 0.77 | 58 | empty |
| 2 | 420 | 0.63 | 0.77 | 45 | empty |
| 3 | 283 | 0.55 | 0.76 | 28 | empty |
| 4 | 295 | 0.53 | 0.75 | 32 | empty |
| 5 | 120 | 0.47 | 0.78 | 18 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1641 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1638 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 831 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 732 Ų buried · 18 hydrogen bonds · protein-nucleic
- E–F · 710 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Compared structures
- 6PUZ · 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 6PUZ · PDBe 6PUZ · UniProt P39476 · UniProt Q76353
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