MolNFT v1 · #108954 · protein
Crystal structure of human wild-type GAPDH at 1.99 ångströms resolution
4WNC · Glyceraldehyde-3-phosphate dehydrogenase: “Crystal structure of human wild-type GAPDH at 1.99 ångströms resolution”. X-ray diffraction, 2 ligands (NAD, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #108954 on GenesisL1: 3D…
- PDB
- 4WNC
- Type
- protein
- Length
- 2,664 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
- Ligands
- NAD, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, A, B, C, D, E, F, G | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 333 | 32% helix, 27% strand | P04406 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains O, C, A, G, B, F, D, E
- ZN · Zinc ion · metal · 6 copies · chains O, E, A, B, C
- ACT · Acetate ion · additive · 2 copies · chains O, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.84 | 0.85 | 99 | empty |
| 2 | 623 | 0.77 | 0.83 | 65 | empty |
| 3 | 632 | 0.75 | 0.81 | 70 | empty |
| 4 | 574 | 0.71 | 0.79 | 69 | NAD |
| 5 | 664 | 0.69 | 0.77 | 71 | NAD |
Interfaces
13 interfaces between chains.
- B–C · 2003 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 2003 Ų buried · 31 hydrogen bonds · protein-protein
- D–G · 1999 Ų buried · 37 hydrogen bonds · protein-protein
- O–F · 1997 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1448 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4WNC · Crystal structure of human wild-type GAPDH at 1.99 angstroms resolution · the same entry in another collection · chain G against G, TM-score 1.00
- P04406 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P04406) · a predicted model of the same protein · chain A 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 4WNC · PDBe 4WNC · UniProt P04406
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.