MolNFT v2 · #20681 · protein
Crystal structure of recombinant photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform, complexed with NADP
1RM4 · Glyceraldehyde 3-phosphate dehydrogenase A: “Crystal structure of recombinant photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform…”. X-ray diffraction at 2, 2 ligands (NDP, SO4), 4 pockets (best druggability 0.71).…
- PDB
- 1RM4
- Type
- protein
- Length
- 1,008 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Spinacia oleracea
- Molecule
- Glyceraldehyde 3-phosphate dehydrogenase A
- EC
- 1.2.1.13
- UniProt
- P19866
- Ligands
- NDP, SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · resolution 2 · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, A, B | Glyceraldehyde 3-phosphate dehydrogenase A (EC 1.2.1.13) | protein | 336 | 30% helix, 27% strand | P19866 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.71 | 0.79 | 63 | SO4, NDP |
| 2 | 572 | 0.71 | 0.79 | 65 | SO4, NDP |
| 3 | 597 | 0.67 | 0.77 | 65 | SO4, NDP |
| 4 | 686 | 0.66 | 0.75 | 56 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1289 Ų buried · 18 hydrogen bonds · protein-protein
- O–A · 376 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1RM4 · Crystal structure of recombinant photosynthetic glyceraldehyde-3- phosphate dehydrogenase… · the same entry in another collection · chain A against A, 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 1RM4 · PDBe 1RM4 · UniProt P19866
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