MolNFT v1 · #165863 · protein + DNA
Cryoem structure of HIV-1 cleaved synaptic complex (csc) intasome
6U8Q · Integrase: “Cryoem structure of HIV-1 cleaved synaptic complex (csc) intasome”. Electron microscopy, 2 ligands (DLU, MG), 20 pockets (best druggability 0.83). MolNFT v1 #165863 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6U8Q
- Type
- protein + DNA
- Length
- 2,538 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; DNA (27-mer); DNA (25-mer)
- EC
- 2.7.7.-
- UniProt
- Q76353
- Ligands
- DLU, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 10 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Integrase (EC 2.7.7.-) | protein | 270 | 43% helix, 21% strand | Q76353 |
| B | Integrase (EC 2.7.7.-) | protein | 264 | 43% helix, 21% strand | Q76353 |
| E, G | DNA (27-mer) | dna | 25 | — | — |
| F, H | DNA (25-mer) | dna | 23 | — | — |
| D | Integrase (EC 2.7.7.-) | protein | 262 | 41% helix, 21% strand | Q76353 |
| I, J | Integrase (EC 2.7.7.-) | protein | 208 | 35% helix, 26% strand | Q76353 |
| K, L | Integrase (EC 2.7.7.-) | protein | 145 | 46% helix, 20% strand | Q76353 |
| M | Integrase (EC 2.7.7.-) | protein | 194 | 26% helix, 27% strand | Q76353 |
| N, O | Integrase (EC 2.7.7.-) | protein | 142 | 42% helix, 20% strand | Q76353 |
| P | Integrase (EC 2.7.7.-) | protein | 192 | 29% helix, 27% strand | Q76353 |
Ligands and binding sites
- DLU · (4r,12as)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6, 8-dioxo-3,4,6,8,12,12A-hexahydro-2H-pyrido[1',2':4, 5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide · ligand · 2 copies · chains A, G, H, E, F, C, M
- MG · Magnesium ion · metal · 4 copies · chains A, H, C
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 | 747 | 0.83 | 0.86 | 83 | empty |
| 2 | 1052 | 0.80 | 0.81 | 116 | empty |
| 3 | 682 | 0.79 | 0.83 | 94 | empty |
| 4 | 564 | 0.78 | 0.84 | 76 | empty |
| 5 | 413 | 0.76 | 0.86 | 59 | empty |
Interfaces
45 interfaces between chains.
- M–N · 2227 Ų buried · 20 hydrogen bonds · protein-protein
- O–P · 1798 Ų buried · 15 hydrogen bonds · protein-protein
- C–I · 1648 Ų buried · 20 hydrogen bonds · protein-protein
- I–K · 1532 Ų buried · 3 hydrogen bonds · protein-protein
- A–J · 1526 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6U8Q · CryoEM structure of HIV-1 cleaved synaptic complex (CSC) intasome · the same entry in another collection · chain A against A, 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 Q76353
- Elsewhere: RCSB PDB 6U8Q · PDBe 6U8Q · UniProt Q76353
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.