Research workbench
GAPDH purified from the supernatant of HEK293F cells: crystal form 3 of 4.
Analyse GAPDH purified from the supernatant of HEK293F cells: crystal form 3 of 4. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YNF
- Type
- protein
- Length
- 2,668 residues
- Chains
- 8
- 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
- P04406
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 334 | 30% helix, 28% strand | P04406 |
| D, E, G, H | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 333 | 29% helix, 27% strand | P04406 |
Ligands and binding sites
- XPE · 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol · additive · 7 copies · chains A, B, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.84 | 0.89 | 64 | empty |
| 2 | 937 | 0.81 | 0.83 | 123 | empty |
| 3 | 303 | 0.78 | 0.90 | 34 | empty |
| 4 | 1141 | 0.75 | 0.78 | 132 | empty |
| 5 | 1123 | 0.75 | 0.77 | 125 | empty |
Interfaces
15 interfaces between chains.
- D–G · 2044 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2040 Ų buried · 29 hydrogen bonds · protein-protein
- E–H · 2032 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 2030 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 1439 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 6YNF · GAPDH purified from the supernatant of HEK293F cells: crystal form 3 of 4. · the same entry in another collection · chain H against H, TM-score 1.00
- P04406 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P04406) · 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 P04406
- Elsewhere: RCSB PDB 6YNF · PDBe 6YNF · UniProt P04406
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