MolNFT v1 · #16336 · protein
Crystal structure of shikimate dehydrogenase (aroe or MJ1084) in complex with NADP+
1NVT · Shikimate 5'-dehydrogenase: “Crystal structure of shikimate dehydrogenase (aroe or MJ1084) in complex with NADP+”. X-ray diffraction, 2 ligands (NAP, ZN), 6 pockets (best druggability 0.74). MolNFT v1 #16336 on GenesisL1: 3D…
- PDB
- 1NVT
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate 5'-dehydrogenase
- EC
- 1.1.1.25
- UniProt
- Q58484
- Ligands
- NAP, ZN
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Shikimate 5'-dehydrogenase (EC 1.1.1.25) | protein | 287 | 39% helix, 20% strand | Q58484 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.74 | 0.83 | 42 | NAP |
| 2 | 455 | 0.65 | 0.78 | 38 | NAP |
| 3 | 93 | 0.42 | 0.78 | 17 | empty |
| 4 | 122 | 0.42 | 0.76 | 16 | empty |
| 5 | 98 | 0.37 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1384 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1NVT · Crystal structure of Shikimate Dehydrogenase (AROE or MJ1084) in complex with NADP+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q58484 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (Q58484) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q58484
- Elsewhere: RCSB PDB 1NVT · PDBe 1NVT · UniProt Q58484
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