MolNFT v1 · #166561 · protein
Native E. COLI glyceraldehyde 3-phosphate dehydrogenase
6UTN · Glyceraldehyde-3-phosphate dehydrogenase: “Native E. COLI glyceraldehyde 3-phosphate dehydrogenase”. X-ray diffraction, 4 ligands (G3P, GLC, NA), 3 pockets (best druggability 0.62). MolNFT v1 #166561 on GenesisL1: 3D structure…
- PDB
- 6UTN
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- A0A0U4BD45
- Ligands
- G3P, GLC, NA, PO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 330 | 31% helix, 28% strand | A0A0U4BD45 |
Ligands and binding sites
- G3P · Sn-glycerol-3-phosphate · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.62 | 0.75 | 60 | empty |
| 2 | 404 | 0.58 | 0.75 | 51 | empty |
| 3 | 390 | 0.56 | 0.74 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 617 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered, oxidation).
Compared structures
- 6UTN · Native E. coli Glyceraldehyde 3-phosphate dehydrogenase · the same entry in another collection · 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 A0A0U4BD45
- Elsewhere: RCSB PDB 6UTN · PDBe 6UTN · UniProt A0A0U4BD45
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