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The three-dimensional structure of shikimate kinase from erwinia chrysanthemi complexed with ADP
Analyse The three-dimensional structure of shikimate kinase from erwinia chrysanthemi… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2SHK
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Erwinia chrysanthemi
- Molecule
- Shikimate kinase
- EC
- 2.7.1.71
- UniProt
- P10880
- Ligands
- ADP, MG
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.6 · 2 distinct chains · 58% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate kinase (EC 2.7.1.71) | protein | 158 | 58% helix, 14% strand | P10880 |
| B | Shikimate kinase (EC 2.7.1.71) | protein | 162 | 59% helix, 14% strand | P10880 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 4 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.63 | 0.89 | 19 | empty |
| 2 | 117 | 0.41 | 0.76 | 25 | MG |
| 3 | 105 | 0.35 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 400 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2SHK · The three-dimensional structure of shikimate kinase from erwinia chrysanthemi complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P10880 · AlphaFold monomer V2.0 prediction for shikimate kinase 2 (P10880) · 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 P10880
- Elsewhere: RCSB PDB 2SHK · PDBe 2SHK · UniProt P10880
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