MolNFT v1 · #35609 · protein
Crystal structure of shikimate 5-dehydrogenase (aroe) from geobacillus kaustophilus
2EGG: “Crystal structure of shikimate 5-dehydrogenase (aroe) from geobacillus kaustophilus”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.67). MolNFT v1 #35609 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2EGG
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate 5-dehydrogenase
- EC
- 1.1.1.25
- UniProt
- Q5KWX7
- Ligands
- CL
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate 5-dehydrogenase (EC 1.1.1.25) | protein | 278 | 40% helix, 19% strand | Q5KWX7 |
| B | Shikimate 5-dehydrogenase (EC 1.1.1.25) | protein | 166 | 43% helix, 18% strand | Q5KWX7 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.67 | 0.80 | 41 | CL |
| 2 | 184 | 0.53 | 0.78 | 24 | empty |
| 3 | 136 | 0.43 | 0.76 | 25 | empty |
| 4 | 97 | 0.39 | 0.76 | 16 | empty |
| 5 | 97 | 0.37 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 940 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2EGG · Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Geobacillus kaustophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5KWX7 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (Q5KWX7) · a predicted model of the same protein · chain B 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 Q5KWX7
- Elsewhere: RCSB PDB 2EGG · PDBe 2EGG · UniProt Q5KWX7
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