Research workbench
Crystal structure of shikimate dehydrogenase (aroe) Y210S mutant from helicobacter pylori in complex with shikimate
Analyse Crystal structure of shikimate dehydrogenase (aroe) Y210S mutant from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FR5
- Type
- protein
- Length
- 526 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
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 263 | 40% helix, 21% strand | P56119 |
Ligands and binding sites
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.76 | 0.84 | 56 | SKM |
| 2 | 404 | 0.75 | 0.85 | 55 | SKM |
| 3 | 366 | 0.60 | 0.77 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 368 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4FR5 · Crystal Structure of Shikimate Dehydrogenase (aroE) Y210S Mutant from Helicobacter pylori… · 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 0.99
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 P56119
- Elsewhere: RCSB PDB 4FR5 · PDBe 4FR5 · UniProt P56119
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