MolNFT v1 · #115036 · protein
Structure of human testis-specific glyceraldehyde-3-phosphate dehydrogenase holo form with NAD+
5C7O · Glyceraldehyde-3-phosphate dehydrogenase, testis-specific: “Structure of human testis-specific glyceraldehyde-3-phosphate dehydrogenase holo form with NAD+”. X-ray diffraction, 2 ligands (NAD, SO4), 3 pockets (best druggability…
- PDB
- 5C7O
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
- EC
- 1.2.1.12
- UniProt
- O14556
- Ligands
- NAD, SO4
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific (EC 1.2.1.12) | protein | 335 | 32% helix, 27% strand | O14556 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains O, P
- SO4 · Sulfate ion · ion · 2 copies · chains O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.65 | 0.77 | 66 | NAD, SO4 |
| 2 | 483 | 0.63 | 0.76 | 48 | NAD, SO4 |
| 3 | 61 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- O–P · 2016 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5C7O · Structure of human testis-specific glyceraldehyde-3-phosphate dehydrogenase holo form… · the same entry in another collection · chain O against O, TM-score 1.00
- O14556 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase… · 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 O14556
- Elsewhere: RCSB PDB 5C7O · PDBe 5C7O · UniProt O14556
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