Research workbench
Crystal structure of shikimate 5-dehydrogenase (aroe) from thermus thermophilus HB8 in complex with shikimate
Analyse Crystal structure of shikimate 5-dehydrogenase (aroe) from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D5C
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate 5-dehydrogenase
- EC
- 1.1.1.25
- UniProt
- Q5SJF8
- Ligands
- SKM, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate 5-dehydrogenase (EC 1.1.1.25) | protein | 261 | 44% helix, 20% strand | Q5SJF8 |
| B | Shikimate 5-dehydrogenase (EC 1.1.1.25) | protein | 259 | 44% helix, 20% strand | Q5SJF8 |
Ligands and binding sites
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.79 | 0.86 | 47 | SKM |
| 2 | 289 | 0.71 | 0.85 | 41 | SKM |
| 3 | 146 | 0.45 | 0.76 | 28 | empty |
| 4 | 148 | 0.44 | 0.75 | 27 | SO4 |
Interfaces
1 interface between chains.
- A–B · 923 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2D5C · Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Thermus Thermophilus HB8 in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SJF8 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (Q5SJF8) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5SJF8
- Elsewhere: RCSB PDB 2D5C · PDBe 2D5C · UniProt Q5SJF8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.