MolNFT v1 · #117156 · protein
1.5 ångström crystal structure of shikimate dehydrogenase 1 from peptoclostridium difficile.
5DZS · Shikimate dehydrogenase (NADP(+)): “1.5 ångström crystal structure of shikimate dehydrogenase 1 from peptoclostridium difficile.”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.79). MolNFT v1 #117156 on…
- PDB
- 5DZS
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate dehydrogenase (NADP(+))
- EC
- 1.1.1.25
- UniProt
- Q187E7
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate dehydrogenase (NADP(+)) (EC 1.1.1.25) | protein | 263 | 42% helix, 21% strand | Q187E7 |
| B | Shikimate dehydrogenase (NADP(+)) (EC 1.1.1.25) | protein | 270 | 39% helix, 21% strand | Q187E7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 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 | 368 | 0.79 | 0.88 | 44 | SO4 |
| 2 | 391 | 0.78 | 0.87 | 56 | SO4 |
| 3 | 512 | 0.75 | 0.83 | 52 | empty |
| 4 | 107 | 0.45 | 0.79 | 17 | empty |
| 5 | 86 | 0.40 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 774 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5DZS · 1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from Peptoclostridium… · 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 Q187E7
- Elsewhere: RCSB PDB 5DZS · PDBe 5DZS · UniProt Q187E7
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