MolNFT v1 · #91949 · protein
Crystal structure of shikimate dehydrogenase (aroe) clinical variant V2356 from helicobacter pylori in complex with shikimate
4FSH: “Crystal structure of shikimate dehydrogenase (aroe) clinical variant V2356 from helicobacter pylori in…”. X-ray diffraction, 1 ligand (SKM), 4 pockets (best druggability 0.78). MolNFT v1 #91949 on GenesisL1: 3D structure, binding…
- PDB
- 4FSH
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate dehydrogenase
- EC
- 1.1.1.25
- UniProt
- P56119
- Ligands
- SKM
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 260 | 38% helix, 19% strand | P56119 |
| B | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 263 | 39% helix, 20% strand | P56119 |
Ligands and binding sites
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.78 | 0.85 | 51 | empty |
| 2 | 405 | 0.78 | 0.87 | 38 | SKM |
| 3 | 99 | 0.42 | 0.77 | 17 | empty |
| 4 | 76 | 0.35 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 656 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4FSH · Crystal Structure of Shikimate Dehydrogenase (aroE) Clinical Variant v2356 from… · the same entry in another collection · chain A against A, TM-score 1.00
- P56119 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (P56119) · a predicted model of the same protein · chain A 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 P56119
- Elsewhere: RCSB PDB 4FSH · PDBe 4FSH · UniProt P56119
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