MolNFT v1 · #80127 · protein
1.45 ångström crystal structure of shikimate 5-dehydrogenase from listeria monocytogenes in complex with shikimate and NAD.
3TNL · Shikimate dehydrogenase: “1.45 ångström crystal structure of shikimate 5-dehydrogenase from listeria monocytogenes in complex with…”. X-ray diffraction, 3 ligands (NAD, SKM, CL), 11 pockets (best druggability 0.79). MolNFT v1 #80127…
- PDB
- 3TNL
- Type
- protein
- Length
- 1,154 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate dehydrogenase
- EC
- 1.1.1.25
- UniProt
- Q8Y9N5
- Ligands
- NAD, SKM, CL
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 288 | 40% helix, 20% strand | Q8Y9N5 |
| B, C | Shikimate dehydrogenase (EC 1.1.1.25) | protein | 289 | 39% helix, 20% strand | Q8Y9N5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains A, C
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.79 | 0.81 | 103 | NAD, SKM |
| 2 | 642 | 0.72 | 0.79 | 57 | NAD, SKM |
| 3 | 627 | 0.70 | 0.78 | 52 | NAD |
| 4 | 603 | 0.69 | 0.77 | 53 | NAD |
| 5 | 202 | 0.48 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1757 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1717 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 807 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3TNL · 1.45 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes… · the same entry in another collection · chain B against B, TM-score 1.00
- Q8Y9N5 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (Q8Y9N5) · a predicted model of the same protein · chain D 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 3TNL · PDBe 3TNL · UniProt Q8Y9N5
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