MolNFT v1 · #91903 · protein
Crystal structure of shikimate dehydrogenase (aroe) Y210S mutant from helicobacter pylori in complex with shikimate
4FR5: “Crystal structure of shikimate dehydrogenase (aroe) Y210S mutant from helicobacter pylori in complex with…”. X-ray diffraction, 1 ligand (SKM), 3 pockets (best druggability 0.76). MolNFT v1 #91903 on GenesisL1: 3D structure, binding…
- PDB
- 4FR5
- Type
- protein
- Length
- 526 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
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 263 | 40% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.76 | 0.84 | 56 | SKM |
| 2 | 404 | 0.75 | 0.85 | 55 | SKM |
| 3 | 366 | 0.60 | 0.77 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 368 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4FR5 · Crystal Structure of Shikimate Dehydrogenase (aroE) Y210S Mutant from Helicobacter pylori… · 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 0.99
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 4FR5 · PDBe 4FR5 · UniProt P56119
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.