Research workbench
The structure of dndg
Analyse The structure of dndg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EXX
- Type
- protein
- Length
- 440 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA phosphorothioation-dependent restriction protein dptg
- UniProt
- A0A0P7R7Y1
- Ligands
- NA
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA phosphorothioation-dependent restriction protein dptg | protein | 440 | 53% helix, 8% strand | A0A0P7R7Y1 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.49 | 0.84 | 21 | empty |
| 2 | 96 | 0.48 | 0.81 | 19 | empty |
| 3 | 83 | 0.44 | 0.80 | 25 | empty |
| 4 | 73 | 0.34 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 7EXX · The structure of DndG · 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
- Every structure of UniProt A0A0P7R7Y1
- Elsewhere: RCSB PDB 7EXX · PDBe 7EXX · UniProt A0A0P7R7Y1
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