Research workbench
Structural basis for shikimate-binding specificity of helicobacter pylori shikimate kinase
Analyse Structural basis for shikimate-binding specificity of helicobacter pylori… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZUI
- Type
- protein
- Length
- 158 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate kinase
- EC
- 2.7.1.71
- UniProt
- P56073
- Ligands
- SKM, PO4
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate kinase (EC 2.7.1.71) | protein | 158 | 56% helix, 15% strand | P56073 |
Ligands and binding sites
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.65 | 0.95 | 17 | SKM |
| 2 | 103 | 0.41 | 0.77 | 19 | PO4 |
Compared structures
- 1ZUI · Structural Basis for Shikimate-binding Specificity of Helicobacter pylori Shikimate Kinase · the same entry in another collection · chain A against A, TM-score 1.00
- P56073 · AlphaFold monomer V2.0 prediction for shikimate kinase (P56073) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P56073
- Elsewhere: RCSB PDB 1ZUI · PDBe 1ZUI · UniProt P56073
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