MolNFT v1 · #174754 · protein
Crystal structure of C150S mutant of glyceraldehyde-3-phosphate- DEHYDROGENASE1 from escherichia COLI complexed with G3P at 2.69 ångström resolution
7C5K · Glyceraldehyde-3-phosphate dehydrogenase: “Crystal structure of C150S mutant of glyceraldehyde-3-phosphate- DEHYDROGENASE1 from escherichia COLI…”. X-ray diffraction, 4 ligands (NAD, G3H, 3PG), 16 pockets (best druggability 0.78).…
- PDB
- 7C5K
- Type
- protein
- Length
- 1,335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- A0A140NCK4
- Ligands
- NAD, G3H, 3PG, PO4
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P, R | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 333 | 30% helix, 28% strand | A0A140NCK4 |
| Q | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 336 | 29% helix, 28% strand | A0A140NCK4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, R, P, Q
- G3H · Glyceraldehyde-3-phosphate · ligand · 2 copies · chains O, P
- 3PG · 3-phosphoglyceric acid · ligand · 2 copies · chains Q, R
- PO4 · Phosphate ion · ion · 5 copies · chains O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.78 | 0.81 | 109 | NAD, G3H, 3PG |
| 2 | 1085 | 0.77 | 0.79 | 111 | NAD, G3H, 3PG |
| 3 | 100 | 0.74 | 0.95 | 29 | PO4 |
| 4 | 520 | 0.63 | 0.75 | 58 | empty |
| 5 | 295 | 0.56 | 0.76 | 33 | empty |
Interfaces
6 interfaces between chains.
- Q–R · 2027 Ų buried · 45 hydrogen bonds · protein-protein
- O–P · 2026 Ų buried · 43 hydrogen bonds · protein-protein
- O–R · 1460 Ų buried · 18 hydrogen bonds · protein-protein
- P–Q · 1446 Ų buried · 20 hydrogen bonds · protein-protein
- O–Q · 582 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7C5K · Crystal Structure of C150S mutant of Glyceraldehyde-3-phosphate-dehydrogenase1 from… · the same entry in another collection · chain O against O, 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 A0A140NCK4
- Elsewhere: RCSB PDB 7C5K · PDBe 7C5K · UniProt A0A140NCK4
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