Research workbench
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle - holo enzyme - at 2.40 ångström resolution
Analyse Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DDI
- Type
- protein
- Length
- 996 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12, 2.6.99.-
- UniProt
- P00355
- Ligands
- NAD, SO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, R, S | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 332 | 30% helix, 26% strand | P00355 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains P, R, S
- SO4 · Sulfate ion · ion · 6 copies · chains P, R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.76 | 0.79 | 126 | SO4, NAD |
| 2 | 466 | 0.62 | 0.76 | 44 | SO4, NAD |
| 3 | 54 | 0.48 | 0.86 | 19 | empty |
| 4 | 75 | 0.40 | 0.79 | 13 | empty |
| 5 | 70 | 0.35 | 0.77 | 13 | empty |
Interfaces
2 interfaces between chains.
- P–R · 1395 Ų buried · 17 hydrogen bonds · protein-protein
- P–S · 522 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DDI · Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle - holo… · the same entry in another collection · chain P against P, TM-score 1.00
- P00355 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P00355) · a predicted model of the same protein · chain P against A, TM-score 0.98
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 P00355
- Elsewhere: RCSB PDB 5DDI · PDBe 5DDI · UniProt P00355
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