Research workbench
The dual coenzyme specificity of photosynthetic glyceraldehyde-3- phosphate dehydrogenase interpreted by the crystal structure of A4 isoform complexed with NAD
Analyse The dual coenzyme specificity of photosynthetic glyceraldehyde-3- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NBO
- Type
- protein
- Length
- 1,010 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase a
- EC
- 1.2.1.13
- UniProt
- P19866
- Ligands
- NAD, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, A | Glyceraldehyde-3-phosphate dehydrogenase a (EC 1.2.1.13) | protein | 337 | 31% helix, 26% strand | P19866 |
| B | Glyceraldehyde-3-phosphate dehydrogenase a (EC 1.2.1.13) | protein | 336 | 30% helix, 25% strand | P19866 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains O, A, B
- SO4 · Sulfate ion · ion · 8 copies · chains O, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.77 | 0.80 | 123 | SO4, NAD |
| 2 | 834 | 0.69 | 0.75 | 68 | empty |
| 3 | 480 | 0.64 | 0.77 | 56 | SO4, NAD |
| 4 | 61 | 0.27 | 0.73 | 16 | NAD |
Interfaces
2 interfaces between chains.
- A–B · 1309 Ų buried · 17 hydrogen bonds · protein-protein
- O–A · 320 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1NBO · The dual coenzyme specificity of photosynthetic glyceraldehyde-3-phosphate dehydrogenase… · the same entry in another collection · chain O against O, TM-score 1.00
- P19866 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase a… · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P19866
- Elsewhere: RCSB PDB 1NBO · PDBe 1NBO · UniProt P19866
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