MolNFT v1 · #181892 · protein + DNA
Atpgs bound tnsc filament from shcast system
7M99: “Atpgs bound tnsc filament from shcast system”. Electron microscopy, 2 ligands (AGS, MG), 20 pockets (best druggability 0.84). MolNFT v1 #181892 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7M99
- Type
- protein + DNA
- Length
- 2,094 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tnsc; DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'); DNA (5'…
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Tnsc | protein | 257 | 52% helix, 9% strand | — |
| I | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 19 | — | — |
| J | DNA (5'- D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | dna | 19 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 7 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F, G, H
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 | 899 | 0.84 | 0.86 | 105 | empty |
| 2 | 667 | 0.81 | 0.86 | 77 | AGS, MG |
| 3 | 651 | 0.80 | 0.85 | 77 | AGS, MG |
| 4 | 537 | 0.80 | 0.87 | 58 | AGS, MG |
| 5 | 559 | 0.80 | 0.86 | 65 | AGS, MG |
Interfaces
27 interfaces between chains.
- F–G · 1223 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1213 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1209 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1209 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1205 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7M99 · ATPgS bound TnsC filament 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 7M99 · PDBe 7M99
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