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Crystal structure of ptdh R301K
Analyse Crystal structure of ptdh R301K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NU6
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphonate dehydrogenase
- EC
- 1.20.1.1
- UniProt
- O69054
- Ligands
- NAD, SO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphonate dehydrogenase (EC 1.20.1.1) | protein | 329 | 37% helix, 17% strand | O69054 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.68 | 0.85 | 43 | NAD, SO4 |
| 2 | 232 | 0.68 | 0.85 | 45 | NAD, SO4 |
| 3 | 69 | 0.52 | 0.86 | 22 | empty |
| 4 | 109 | 0.47 | 0.79 | 20 | empty |
| 5 | 74 | 0.37 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2731 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
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 O69054
- Elsewhere: RCSB PDB 4NU6 · PDBe 4NU6 · UniProt O69054
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