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Crystal Structure of Mycobacterium tuberculosis Shikimate Dehydrogenase
Analyse Crystal Structure of Mycobacterium tuberculosis Shikimate Dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P4L
- Type
- protein
- Length
- 784 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.009
- Source
- Mycobacterium tuberculosis
- Molecule
- Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
- EC
- 1.1.1.25
- UniProt
- P95001
- Ligands
- SKM, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.009 · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase) (EC 1.1.1.25) | protein | 264 | 44% helix, 21% strand | P95001 |
| B | Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase) (EC 1.1.1.25) | protein | 257 | 42% helix, 21% strand | P95001 |
| C | Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase) (EC 1.1.1.25) | protein | 263 | 45% helix, 21% strand | P95001 |
Ligands and binding sites
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.77 | 0.79 | 106 | empty |
| 2 | 312 | 0.66 | 0.81 | 31 | SKM |
| 3 | 367 | 0.66 | 0.80 | 35 | SKM |
| 4 | 344 | 0.65 | 0.80 | 33 | SKM |
| 5 | 72 | 0.39 | 0.79 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 399 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 168 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 76 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4P4L · Crystal structure of mycobacterium tuberculosis shikimate dehydrogenase · 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 P95001
- Elsewhere: RCSB PDB 4P4L · PDBe 4P4L · UniProt P95001
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