MolNFT v1 · #182850 · protein + DNA
ATP-bound tnsc-tniq complex from shcast system
7N6I · Tniq (homology model): “ATP-bound tnsc-tniq complex from shcast system”. Electron microscopy, 2 ligands (ATP, MG), 20 pockets (best druggability 0.82). MolNFT v1 #182850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7N6I
- Type
- protein + DNA
- Length
- 2,392 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tniq (homology model); Tnsc; DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*…
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tniq (homology model) | protein | 151 | 32% helix, 9% strand | — |
| C, D, E, F, G, H, I, J | Tnsc | protein | 257 | 52% helix, 9% strand | — |
| K | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 17 | — | — |
| L | DNA (5'- D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | dna | 17 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 7 copies · chains C, D, E, F, G, H, I, J
- MG · Magnesium ion · metal · 7 copies · chains C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.82 | 0.84 | 139 | empty |
| 2 | 735 | 0.82 | 0.85 | 76 | ATP, MG |
| 3 | 786 | 0.81 | 0.84 | 88 | ATP, MG |
| 4 | 581 | 0.81 | 0.86 | 63 | ATP, MG |
| 5 | 1087 | 0.81 | 0.82 | 123 | empty |
Interfaces
32 interfaces between chains.
- H–I · 1222 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1220 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1207 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1207 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1205 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7N6I · ATP-bound TnsC-TniQ complex from ShCAST system · 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
- Elsewhere: RCSB PDB 7N6I · PDBe 7N6I
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