Research workbench
Crystal structure of the T229K mutant of human GAPDH at 2.3 angstroems resolution
Analyse Crystal structure of the T229K mutant of human GAPDH at 2.3 angstroems… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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