Research workbench
Cryo-EM structure of rous sarcoma virus cleaved synaptic complex (csc) with HIV-1 integrase strand transfer inhibitor mk-2048
Analyse Cryo-EM structure of rous sarcoma virus cleaved synaptic complex (csc) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JN3
- Type
- protein + DNA
- Length
- 1,875 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; DNA (5'- D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*T)-3'); DNA…
- EC
- 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-
- UniProt
- P03354
- Ligands
- ZZX, MG, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Integrase (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 269 | 36% helix, 21% strand | P03354 |
| B | Integrase (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 213 | 34% helix, 24% strand | P03354 |
| C | Integrase (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 210 | 30% helix, 24% strand | P03354 |
| D | Integrase (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 212 | 27% helix, 17% strand | P03354 |
| F | Integrase (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 214 | 31% helix, 25% strand | P03354 |
| G, H | Integrase (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 210 | 32% helix, 24% strand | P03354 |
| I, K | DNA (5'- D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*T)-3') | dna | 18 | — | — |
| J, L | DNA (5'-D(*AP*TP*TP*GP*CP*AP*TP*AP*AP*GP*AP*CP*AP*AP*CP*A)- 3') | dna | 16 | — | — |
Ligands and binding sites
- ZZX · (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N, 6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1', 2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide · ligand · 2 copies · chains A, I, J, E, K, L
- MG · Magnesium ion · metal · 4 copies · chains A, E
- ZN · Zinc ion · metal · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.82 | 0.85 | 64 | empty |
| 2 | 994 | 0.82 | 0.83 | 83 | empty |
| 3 | 988 | 0.81 | 0.83 | 80 | empty |
| 4 | 1034 | 0.81 | 0.82 | 69 | empty |
| 5 | 635 | 0.79 | 0.84 | 53 | empty |
Interfaces
32 interfaces between chains.
- C–D · 1800 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1792 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1758 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1069 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 1064 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7JN3 · Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1… · 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 P03354
- Elsewhere: RCSB PDB 7JN3 · PDBe 7JN3 · UniProt P03354
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.