MolNFT v1 · #181893 · protein + DNA
ADP-ALF3 bound tnsc structure from shcast system
7M9A: “ADP-ALF3 bound tnsc structure from shcast system”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.83). MolNFT v1 #181893 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7M9A
- Type
- protein + DNA
- Length
- 3,138 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tnsc; DNA (27-mer)
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.83
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, I, J, K, L | Tnsc | protein | 257 | 52% helix, 9% strand | — |
| M | DNA (27-mer) | dna | 27 | — | — |
| N | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 10 copies · chains B, C, D, E, F, H, I, J, K, L
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 | 610 | 0.83 | 0.89 | 88 | empty |
| 2 | 540 | 0.83 | 0.89 | 70 | empty |
| 3 | 621 | 0.81 | 0.86 | 78 | ADP |
| 4 | 952 | 0.79 | 0.81 | 85 | ADP |
| 5 | 1034 | 0.79 | 0.81 | 95 | ADP |
Interfaces
48 interfaces between chains.
- M–N · 1122 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- B–C · 933 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 922 Ų buried · 20 hydrogen bonds · protein-protein
- K–L · 916 Ų buried · 8 hydrogen bonds · protein-protein
- J–K · 882 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7M9A · ADP-AlF3 bound TnsC structure 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 7M9A · PDBe 7M9A
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