Research workbench
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle complexed with orthophenanthroline at 1.90 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
- 5TSO
- 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
- PHN, NAD, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% 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 | 32% helix, 27% strand | P00355 |
Ligands and binding sites
- PHN · 1,10-phenanthroline · ligand · 4 copies · chains R, S
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains P, R, S
- SO4 · Sulfate ion · ion · 11 copies · chains P, R, S
- GOL · Glycerol · additive · 7 copies · chains P, R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.77 | 0.79 | 124 | SO4, NAD |
| 2 | 531 | 0.66 | 0.77 | 58 | SO4, NAD |
| 3 | 83 | 0.30 | 0.72 | 21 | empty |
| 4 | 53 | 0.30 | 0.76 | 12 | empty |
Interfaces
2 interfaces between chains.
- P–R · 1409 Ų buried · 22 hydrogen bonds · protein-protein
- P–S · 608 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5TSO · Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle complexed… · 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 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 P00355
- Elsewhere: RCSB PDB 5TSO · PDBe 5TSO · UniProt P00355
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