MolNFT v1 · #134476 · protein
Crystal structure of a semialdehyde dehydrogenase NAD-binding protein from cupriavidus necator in complex with calcium and NAD
5T57: “Crystal structure of a semialdehyde dehydrogenase NAD-binding protein from cupriavidus necator in complex…”. X-ray diffraction, 3 ligands (NAD, CA, ZN), 3 pockets (best druggability 0.60). MolNFT v1 #134476 on GenesisL1: 3D…
- PDB
- 5T57
- Type
- protein
- Length
- 276 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semialdehyde dehydrogenase NAD-binding protein
- UniProt
- F8GV06
- Ligands
- NAD, CA, ZN
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semialdehyde dehydrogenase NAD-binding protein | protein | 276 | 51% helix, 15% strand | F8GV06 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- CA · Calcium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.60 | 0.73 | 46 | empty |
| 2 | 121 | 0.42 | 0.76 | 20 | NAD, ZN |
| 3 | 60 | 0.31 | 0.75 | 15 | empty |
Compared structures
- 5T57 · Crystal Structure of a Semialdehyde dehydrogenase NAD-binding Protein from Cupriavidus… · the same entry in another collection · chain A against A, TM-score 1.00
- F8GV06 · AlphaFold monomer V2.0 prediction for D-apionate oxidoisomerase (F8GV06) · 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 F8GV06
- Elsewhere: RCSB PDB 5T57 · PDBe 5T57 · UniProt F8GV06
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