Research workbench
Crystal structure of shikimate dehydrogenase (aroe) clinical variant V2356 from helicobacter pylori in complex with shikimate
Analyse Crystal structure of shikimate dehydrogenase (aroe) clinical variant V2356 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FSH
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate dehydrogenase
- EC
- 1.1.1.25
- UniProt
- P56119
- Ligands
- SKM
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 260 | 38% helix, 19% strand | P56119 |
| B | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 263 | 39% helix, 20% strand | P56119 |
Ligands and binding sites
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.78 | 0.85 | 51 | empty |
| 2 | 405 | 0.78 | 0.87 | 38 | SKM |
| 3 | 99 | 0.42 | 0.77 | 17 | empty |
| 4 | 76 | 0.35 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 656 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4FSH · Crystal Structure of Shikimate Dehydrogenase (aroE) Clinical Variant v2356 from… · the same entry in another collection · chain A against A, TM-score 1.00
- P56119 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (P56119) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P56119
- Elsewhere: RCSB PDB 4FSH · PDBe 4FSH · UniProt P56119
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