MolNFT v1 · #80175 · protein
2.2 ångström crystal structure of shikimate 5-dehydrogenase from listeria monocytogenes in complex with NAD.
3TOZ · Shikimate dehydrogenase: “2.2 ångström crystal structure of shikimate 5-dehydrogenase from listeria monocytogenes in complex with NAD.”. X-ray diffraction, 3 ligands (NAD, SO4, CL), 20 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 3TOZ
- Type
- protein
- Length
- 2,315 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate dehydrogenase
- EC
- 1.1.1.25
- UniProt
- Q8Y9N5
- Ligands
- NAD, SO4, CL
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, H | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 291 | 40% helix, 20% strand | Q8Y9N5 |
| B | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 290 | 40% helix, 20% strand | Q8Y9N5 |
| C, F | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 287 | 40% helix, 20% strand | Q8Y9N5 |
| D, E | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 289 | 41% helix, 20% strand | Q8Y9N5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, F, G, H
- CL · Chloride ion · ion · 4 copies · chains C, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.70 | 0.77 | 59 | NAD, SO4 |
| 2 | 571 | 0.69 | 0.78 | 51 | NAD, SO4 |
| 3 | 570 | 0.68 | 0.78 | 52 | NAD |
| 4 | 589 | 0.68 | 0.77 | 51 | NAD, SO4 |
| 5 | 340 | 0.67 | 0.81 | 46 | NAD |
Interfaces
13 interfaces between chains.
- A–B · 1713 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1706 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1652 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1620 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 756 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3TOZ · 2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes… · the same entry in another collection · chain H against H, TM-score 1.00
- Q8Y9N5 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (Q8Y9N5) · a predicted model of the same protein · chain C 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 Q8Y9N5
- Elsewhere: RCSB PDB 3TOZ · PDBe 3TOZ · UniProt Q8Y9N5
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