MolNFT v1 · #20676 · protein
Crystal structure of mutant S188A of photosynthetic glyceraldehyde-3- phosphate dehydrogenase A4 isoform, complexed with NADP
1RM5 · Glyceraldehyde 3-phosphate dehydrogenase a: “Crystal structure of mutant S188A of photosynthetic glyceraldehyde-3- phosphate dehydrogenase A4 isoform…”. X-ray diffraction, 2 ligands (NDP, SO4), 5 pockets (best druggability 0.70).…
- PDB
- 1RM5
- Type
- protein
- Length
- 1,011 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
- NDP, SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 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 | 337 | 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 · 10 copies · chains O, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.70 | 0.77 | 63 | SO4, NDP |
| 2 | 762 | 0.69 | 0.76 | 76 | SO4, NDP |
| 3 | 642 | 0.65 | 0.75 | 53 | empty |
| 4 | 452 | 0.62 | 0.76 | 50 | SO4, NDP |
| 5 | 52 | 0.25 | 0.73 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1297 Ų buried · 16 hydrogen bonds · protein-protein
- O–A · 371 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1RM5 · Crystal structure of mutant S188A of photosynthetic glyceraldehyde-3-phosphate… · 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 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 P19866
- Elsewhere: RCSB PDB 1RM5 · PDBe 1RM5 · UniProt P19866
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