MolNFT v1 · #75143 · protein
Shikimate 5-dehydrogenase (aroe) from helicobacter pylori in complex with shikimate and NADPH
3PHI · Shikimate dehydrogenase: “Shikimate 5-dehydrogenase (aroe) from helicobacter pylori in complex with shikimate and NADPH”. X-ray diffraction, 2 ligands (SKM, NDP), 2 pockets (best druggability 0.73). MolNFT v1 #75143 on GenesisL1: 3D…
- PDB
- 3PHI
- Type
- protein
- Length
- 518 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, NDP
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 259 | 39% helix, 21% strand | P56119 |
Ligands and binding sites
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.73 | 0.84 | 52 | SKM, NDP |
| 2 | 554 | 0.73 | 0.81 | 71 | SKM, NDP |
Interfaces
1 interface between chains.
- A–B · 166 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3PHI · Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate and… · 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 B against A, TM-score 0.99
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 3PHI · PDBe 3PHI · UniProt P56119
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