Research workbench
Crystal structure of human glycerol-3-phosphate dehydrogenase 1-like protein
Analyse Crystal structure of human glycerol-3-phosphate dehydrogenase 1-like protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PLA
- Type
- protein
- Length
- 686 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-3-phosphate dehydrogenase 1-like protein
- UniProt
- Q8N335
- Ligands
- NAD, PO4, CL
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycerol-3-phosphate dehydrogenase 1-like protein | protein | 343 | 53% helix, 15% strand | Q8N335 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.81 | 0.90 | 49 | PO4, NAD |
| 2 | 391 | 0.80 | 0.89 | 44 | PO4, NAD |
| 3 | 56 | 0.39 | 0.81 | 13 | empty |
| 4 | 73 | 0.33 | 0.75 | 16 | empty |
| 5 | 55 | 0.31 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1701 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 2PLA · Crystal structure of human glycerol-3-phosphate dehydrogenase 1-like protein · the same entry in another collection · chain B against B, TM-score 1.00
- Q8N335 · AlphaFold monomer V2.0 prediction for glycerol-3-phosphate dehydrogenase 1-like protein… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8N335
- Elsewhere: RCSB PDB 2PLA · PDBe 2PLA · UniProt Q8N335
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