Research workbench
Crystal structure of the rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
Analyse Crystal structure of the rabbit muscle glyceraldehyde-3-phosphate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J0X
- Type
- protein
- Length
- 1,328 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- P46406
- Ligands
- NAD
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P, Q, R | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 332 | 32% helix, 27% strand | P46406 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains P, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.80 | 0.81 | 124 | empty |
| 2 | 1111 | 0.74 | 0.77 | 118 | NAD |
| 3 | 573 | 0.67 | 0.77 | 62 | NAD |
| 4 | 532 | 0.65 | 0.76 | 63 | empty |
| 5 | 77 | 0.33 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- O–P · 2060 Ų buried · 28 hydrogen bonds · protein-protein
- Q–R · 2041 Ų buried · 28 hydrogen bonds · protein-protein
- O–R · 1357 Ų buried · 23 hydrogen bonds · protein-protein
- P–Q · 1316 Ų buried · 21 hydrogen bonds · protein-protein
- O–Q · 501 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 1J0X · Crystal structure of the rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH) · the same entry in another collection · chain R against R, TM-score 1.00
- P46406 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P46406) · a predicted model of the same protein · chain R 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 P46406
- Elsewhere: RCSB PDB 1J0X · PDBe 1J0X · UniProt P46406
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