Research workbench
Crystal structures of glyceraldehyde-3-phosphate dehydrogenase complexes with NAD
Analyse Crystal structures of glyceraldehyde-3-phosphate dehydrogenase complexes with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V1Y
- Type
- protein
- Length
- 1,343 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase, cytosolic
- EC
- 1.2.1.12
- UniProt
- Q0J8A4
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, B, C | Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) | protein | 336 | 32% helix, 28% strand | Q0J8A4 |
| A | Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) | protein | 335 | 31% helix, 27% strand | Q0J8A4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.76 | 0.79 | 116 | NAD |
| 2 | 518 | 0.70 | 0.80 | 56 | empty |
| 3 | 544 | 0.70 | 0.79 | 61 | NAD |
| 4 | 483 | 0.69 | 0.80 | 59 | empty |
| 5 | 523 | 0.68 | 0.79 | 56 | NAD |
Interfaces
6 interfaces between chains.
- A–B · 2013 Ų buried · 34 hydrogen bonds · protein-protein
- O–C · 1999 Ų buried · 35 hydrogen bonds · protein-protein
- O–B · 1435 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1424 Ų buried · 24 hydrogen bonds · protein-protein
- O–A · 524 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3V1Y · Crystal structures of glyceraldehyde-3-phosphate dehydrogenase complexes with NAD · the same entry in another collection · chain C against C, TM-score 1.00
- Q0J8A4 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase 1… · 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 Q0J8A4
- Elsewhere: RCSB PDB 3V1Y · PDBe 3V1Y · UniProt Q0J8A4
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