MolNFT v1 · #25185 · protein
Crystal structure of shikimate-5-dehydrogenase with NAD
1VI2 · Shikimate 5-dehydrogenase 2: “Crystal structure of shikimate-5-dehydrogenase with NAD”. X-ray diffraction, 2 ligands (NAD, SO4), 6 pockets (best druggability 0.75). MolNFT v1 #25185 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1VI2
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate 5-dehydrogenase 2
- EC
- 1.1.1.25
- UniProt
- P0A6D5
- Ligands
- NAD, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate 5-dehydrogenase 2 (EC 1.1.1.25) | protein | 284 | 40% helix, 20% strand | P0A6D5 |
| B | Shikimate 5-dehydrogenase 2 (EC 1.1.1.25) | protein | 282 | 43% helix, 21% strand | P0A6D5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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 | 724 | 0.75 | 0.80 | 56 | SO4, NAD |
| 2 | 717 | 0.71 | 0.78 | 61 | SO4, NAD |
| 3 | 182 | 0.44 | 0.74 | 27 | empty |
| 4 | 90 | 0.36 | 0.75 | 18 | empty |
| 5 | 53 | 0.32 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 838 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
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 P0A6D5
- Elsewhere: RCSB PDB 1VI2 · PDBe 1VI2 · UniProt P0A6D5
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