MolNFT v1 · #16118 · protein
X-ray structure of shikimate dehydrogenase complexed with NAD+ from E.COLI (ydib) northeast structural genomics research consortium (nesg) target ER24
1NPD · Hypothetical shikimate 5-dehydrogenase-like protein ydib: “X-ray structure of shikimate dehydrogenase complexed with NAD+ from E.COLI (ydib) northeast structural…”. X-ray diffraction, 1 ligand (NAD), 3 pockets (best druggability…
- PDB
- 1NPD
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical shikimate 5-dehydrogenase-like protein ydib
- EC
- 1.1.1.25
- UniProt
- P0A6D5
- Ligands
- NAD
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical shikimate 5-dehydrogenase-like protein ydib (EC 1.1.1.25) | protein | 287 | 38% helix, 20% strand | P0A6D5 |
| B | Hypothetical shikimate 5-dehydrogenase-like protein ydib (EC 1.1.1.25) | protein | 288 | 39% helix, 19% strand | P0A6D5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.73 | 0.79 | 64 | NAD |
| 2 | 672 | 0.70 | 0.78 | 64 | NAD |
| 3 | 86 | 0.35 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1392 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 1NPD · X-ray structure of shikimate dehydrogenase complexed with NAD+ from E.COLI (ydib)… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6D5 · AlphaFold monomer V2.0 prediction for QUINATE/SHIKIMATE dehydrogenase (P0A6D5) · 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 P0A6D5
- Elsewhere: RCSB PDB 1NPD · PDBe 1NPD · UniProt P0A6D5
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