Research workbench
Structure of thermotoga maritima disa D75N mutant with reaction product C-di-AMP
Analyse Structure of thermotoga maritima disa D75N mutant with reaction product C-di-AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YXM
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA integrity scanning protein disa
- EC
- 2.7.7.85
- UniProt
- Q9WY43
- Ligands
- 2BA
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA integrity scanning protein disa (EC 2.7.7.85) | protein | 349 | 59% helix, 12% strand | Q9WY43 |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.76 | 0.81 | 80 | 2BA, MPD |
| 2 | 115 | 0.42 | 0.76 | 21 | empty |
| 3 | 94 | 0.41 | 0.77 | 23 | empty |
| 4 | 80 | 0.34 | 0.75 | 14 | empty |
| 5 | 80 | 0.34 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 465 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4YXM · Structure of Thermotoga maritima DisA D75N mutant with reaction product c-di-AMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WY43 · AlphaFold monomer V2.0 prediction for DNA integrity scanning protein disa (Q9WY43) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9WY43
- Elsewhere: RCSB PDB 4YXM · PDBe 4YXM · UniProt Q9WY43
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.