MolNFT v1 · #188659 · protein + DNA
Mvv cleaved synaptic complex (csc) intasome at 3.4 a resolution
7U32 · Integrase: “Mvv cleaved synaptic complex (csc) intasome at 3.4 a resolution”. Electron microscopy, 2 ligands (ZN, CA), 20 pockets (best druggability 0.87). MolNFT v1 #188659 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7U32
- Type
- protein + DNA
- Length
- 3,866 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; DNA EV273; DNA EV272
- EC
- 2.7.7.-, 3.1.-.-
- UniProt
- P35956
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Integrase (EC 2.7.7.-, 3.1.-.-) | protein | 276 | 39% helix, 22% strand | P35956 |
| B, J | Integrase (EC 2.7.7.-, 3.1.-.-) | protein | 204 | 53% helix, 16% strand | P35956 |
| C, K | Integrase (EC 2.7.7.-, 3.1.-.-) | protein | 262 | 41% helix, 19% strand | P35956 |
| D, H, L, P | Integrase (EC 2.7.7.-, 3.1.-.-) | protein | 217 | 39% helix, 28% strand | P35956 |
| E, M | Integrase (EC 2.7.7.-, 3.1.-.-) | protein | 260 | 42% helix, 21% strand | P35956 |
| F, N | Integrase (EC 2.7.7.-, 3.1.-.-) | protein | 261 | 41% helix, 22% strand | P35956 |
| G, O | Integrase (EC 2.7.7.-, 3.1.-.-) | protein | 204 | 50% helix, 13% strand | P35956 |
| X, Y | DNA EV273 | dna | 17 | — | — |
| W, Z | DNA EV272 | dna | 15 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, E, F, G, I, J, K, M, N, O
- CA · Calcium ion · metal · 2 copies · chains A, Z, W, I
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 | 772 | 0.87 | 0.90 | 107 | empty |
| 2 | 1137 | 0.83 | 0.84 | 83 | empty |
| 3 | 1126 | 0.83 | 0.84 | 88 | empty |
| 4 | 879 | 0.83 | 0.85 | 116 | empty |
| 5 | 773 | 0.82 | 0.85 | 95 | empty |
Interfaces
65 interfaces between chains.
- J–K · 1527 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1520 Ų buried · 8 hydrogen bonds · protein-protein
- M–N · 1472 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 1468 Ų buried · 2 hydrogen bonds · protein-protein
- I–J · 1422 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7U32 · MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution · 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 P35956
- Elsewhere: RCSB PDB 7U32 · PDBe 7U32 · UniProt P35956
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.