MolNFT v1 · #34420 · protein
Crystal structure of the diadenosine tetraphosphate hydrolase from shigella flexneri 2A
2DFJ · Diadenosinetetraphosphatase: “Crystal structure of the diadenosine tetraphosphate hydrolase from shigella flexneri 2A”. X-ray diffraction, 1 ligand (MN), 2 pockets (best druggability 0.59). MolNFT v1 #34420 on GenesisL1: 3D…
- PDB
- 2DFJ
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diadenosinetetraphosphatase
- EC
- 3.6.1.41
- Ligands
- MN
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diadenosinetetraphosphatase (EC 3.6.1.41) | protein | 267 | 35% helix, 18% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.59 | 0.75 | 47 | MN |
| 2 | 335 | 0.59 | 0.77 | 44 | MN |
Interfaces
1 interface between chains.
- A–B · 461 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2DFJ · Crystal Structure of the Diadenosine Tetraphosphate Hydrolase from Shigella flexneri 2a · 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 2DFJ · PDBe 2DFJ
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