Research workbench
Shikimate kinase from mycobacterium tuberculosis in complex with shikimate
Analyse Shikimate kinase from mycobacterium tuberculosis in complex with shikimate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IYR
- Type
- protein
- Length
- 331 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate kinase
- EC
- 2.7.1.71
- UniProt
- P0A4Z2
- Ligands
- SKM
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate kinase (EC 2.7.1.71) | protein | 164 | 57% helix, 12% strand | P0A4Z2 |
| B | Shikimate kinase (EC 2.7.1.71) | protein | 167 | 56% helix, 12% strand | P0A4Z2 |
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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.69 | 0.74 | 70 | SKM |
| 2 | 231 | 0.53 | 0.76 | 29 | SKM |
Interfaces
1 interface between chains.
- A–B · 222 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2IYR · Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate · the same entry in another collection · chain A against A, TM-score 1.00
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 P0A4Z2
- Elsewhere: RCSB PDB 2IYR · PDBe 2IYR · UniProt P0A4Z2
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