Research workbench
Crystal structure of shikimate dehydrogenase from aquifex aeolicus at 2.35 ångström resolution
Analyse Crystal structure of shikimate dehydrogenase from aquifex aeolicus at 2.35… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HK8
- Type
- protein
- Length
- 2,125 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate dehydrogenase
- EC
- 1.1.1.25
- UniProt
- O67049
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, H | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 266 | 40% helix, 20% strand | O67049 |
| C | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 265 | 40% helix, 20% strand | O67049 |
| F | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 264 | 40% helix, 20% strand | O67049 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.74 | 0.77 | 90 | empty |
| 2 | 818 | 0.73 | 0.78 | 66 | empty |
| 3 | 484 | 0.72 | 0.82 | 47 | empty |
| 4 | 398 | 0.72 | 0.83 | 40 | empty |
| 5 | 495 | 0.71 | 0.81 | 53 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1267 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1254 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1248 Ų buried · 2 hydrogen bonds · protein-protein
- G–H · 1244 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 519 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2HK8 · Crystal structure of shikimate dehydrogenase from aquifex aeolicus at 2.35 angstrom… · the same entry in another collection · chain H against H, TM-score 1.00
- O67049 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (O67049) · a predicted model of the same protein · 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 O67049
- Elsewhere: RCSB PDB 2HK8 · PDBe 2HK8 · UniProt O67049
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