Research workbench
Crystal structure of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase (gapds) complex with NAD, a binary form
Analyse Crystal structure of human sperm-specific glyceraldehyde-3-phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PFW
- Type
- protein
- Length
- 672 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
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 33% 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 | 336 | 33% helix, 27% strand | O14556 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains O, P
- GOL · Glycerol · additive · 5 copies · chains O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 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 | 0.65 | 0.76 | 54 | NAD, GOL |
| 2 | 437 | 0.64 | 0.77 | 43 | NAD, GOL |
| 3 | 66 | 0.33 | 0.76 | 16 | empty |
| 4 | 53 | 0.30 | 0.76 | 18 | NAD |
| 5 | 63 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- O–P · 2059 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3PFW · Crystal structure of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase… · 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 0.99
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 3PFW · PDBe 3PFW · UniProt O14556
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