Research workbench
Crystal structure of phosphorylated mutant of glyceraldehyde 3- phosphate dehydrogenase from human placenta at 3.15A resolution
Analyse Crystal structure of phosphorylated mutant of glyceraldehyde 3- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ADE
- Type
- protein
- Length
- 999 residues
- Chains
- 3
- 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
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 333 | 31% helix, 28% strand | P04406 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.60 | 0.77 | 39 | NAD |
| 2 | 539 | 0.59 | 0.73 | 41 | empty |
| 3 | 329 | 0.59 | 0.77 | 30 | empty |
| 4 | 356 | 0.58 | 0.76 | 49 | empty |
| 5 | 111 | 0.34 | 0.72 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–B · 604 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 137 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 6ADE · Crystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase… · the same entry in another collection · chain A against A, 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 6ADE · PDBe 6ADE · UniProt P04406
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