Research workbench
Comparison of the structures of wild type and a N313T mutant of escherichia COLI glyceraldehyde 3-phosphate dehydrogenases: implication for NAD binding and cooperativity
Analyse Comparison of the structures of wild type and a N313T mutant of escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GAD
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- P0A9B2
- Ligands
- NAD
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P | D-glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 330 | 29% helix, 28% strand | P0A9B2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.66 | 0.77 | 52 | NAD |
| 2 | 523 | 0.63 | 0.76 | 48 | NAD |
| 3 | 54 | 0.32 | 0.77 | 17 | NAD |
| 4 | 55 | 0.32 | 0.77 | 15 | empty |
| 5 | 65 | 0.32 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- O–P · 2033 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1GAD · Comparison of the structures of wild type and a N313T mutant of escherichia COLI… · the same entry in another collection · chain O against O, TM-score 1.00
- P0A9B2 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase a (P0A9B2) · a predicted model of the same protein · chain P 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 P0A9B2
- Elsewhere: RCSB PDB 1GAD · PDBe 1GAD · UniProt P0A9B2
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