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Structure of shikimate kinase from mycobacterium tuberculosis complexed with ADP and mg at 2.8 angstrons of resolution
Analyse Structure of shikimate kinase from mycobacterium tuberculosis complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DFT
- Type
- protein
- Length
- 641 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate kinase
- EC
- 2.7.1.71
- UniProt
- P0A4Z2
- Ligands
- ADP, MG, CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate kinase (EC 2.7.1.71) | protein | 156 | 59% helix, 12% strand | P0A4Z2 |
| B, D | Shikimate kinase (EC 2.7.1.71) | protein | 165 | 53% helix, 12% strand | P0A4Z2 |
| C | Shikimate kinase (EC 2.7.1.71) | protein | 155 | 53% helix, 12% strand | P0A4Z2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.81 | 0.84 | 89 | MG, ADP, CL |
| 2 | 679 | 0.78 | 0.83 | 74 | ADP, MG, CL |
| 3 | 433 | 0.70 | 0.81 | 56 | empty |
| 4 | 166 | 0.59 | 0.83 | 29 | MG, CL |
| 5 | 203 | 0.57 | 0.80 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–C · 910 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 519 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 486 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 423 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 151 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2DFT · Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and Mg… · 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 2DFT · PDBe 2DFT · UniProt P0A4Z2
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