MolNFT v1 · #108960 · protein
Crystal structure of the T229K mutant of human GAPDH at 2.3 angstroems resolution
4WNI · Glyceraldehyde-3-phosphate dehydrogenase: “Crystal structure of the T229K mutant of human GAPDH at 2.3 angstroems resolution”. X-ray diffraction, 2 ligands (NAD, ZN), 11 pockets (best druggability 0.81). MolNFT v1 #108960 on…
- PDB
- 4WNI
- Type
- protein
- Length
- 1,332 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, 2.6.99.-
- UniProt
- P04406
- Ligands
- NAD, ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, A, B, C | 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 · 3 copies · chains O, C, A, B
- ZN · Zinc ion · metal · 3 copies · chains O, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.81 | 0.83 | 119 | empty |
| 2 | 497 | 0.71 | 0.81 | 60 | NAD |
| 3 | 484 | 0.68 | 0.79 | 59 | NAD |
| 4 | 572 | 0.68 | 0.78 | 62 | NAD |
| 5 | 573 | 0.66 | 0.76 | 63 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2038 Ų buried · 31 hydrogen bonds · protein-protein
- O–B · 2036 Ų buried · 30 hydrogen bonds · protein-protein
- O–C · 1443 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1441 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 452 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4WNI · Crystal structure of the T229K mutant of human GAPDH at 2.3 angstroems resolution · the same entry in another collection · chain C against C, 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 4WNI · PDBe 4WNI · UniProt P04406
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