Research workbench
Cryo-EM structure of rous sarcoma virus cleaved synaptic complex (csc) with HIV-1 integrase strand transfer inhibitor mk-2048. cluster identified by 3-dimensional variability analysis in cryosparc.
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
- 7KU7
- 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
- 2.7.7.-
- UniProt
- P03354
- Ligands
- ZZX, MG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Integrase (EC 2.7.7.-) | protein | 269 | 38% helix, 21% strand | P03354 |
| B | Integrase (EC 2.7.7.-) | protein | 213 | 33% helix, 27% strand | P03354 |
| C | Integrase (EC 2.7.7.-) | protein | 210 | 30% helix, 25% strand | P03354 |
| D | Integrase (EC 2.7.7.-) | protein | 212 | 29% helix, 21% strand | P03354 |
| F | Integrase (EC 2.7.7.-) | protein | 214 | 30% helix, 26% strand | P03354 |
| G, H | Integrase (EC 2.7.7.-) | protein | 210 | 34% helix, 26% 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, J, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.84 | 0.85 | 102 | empty |
| 2 | 960 | 0.84 | 0.85 | 96 | empty |
| 3 | 1150 | 0.81 | 0.82 | 76 | empty |
| 4 | 722 | 0.80 | 0.84 | 68 | empty |
| 5 | 515 | 0.80 | 0.86 | 65 | empty |
Interfaces
32 interfaces between chains.
- C–D · 1792 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1741 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1693 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1100 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 1012 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7KU7 · 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 7KU7 · PDBe 7KU7 · UniProt P03354
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