Research workbench
Crystal structure of glycerol-3-phosphate dehydrogenase (TM0378) from thermotoga maritima at 2.00 a resolution
Analyse Crystal structure of glycerol-3-phosphate dehydrogenase (TM0378) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z82
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-3-phosphate dehydrogenase
- EC
- 1.1.1.8
- Ligands
- NDP, G3H, G3P
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol-3-phosphate dehydrogenase (EC 1.1.1.8) | protein | 312 | 53% helix, 13% strand | — |
| B | Glycerol-3-phosphate dehydrogenase (EC 1.1.1.8) | protein | 312 | 54% helix, 13% strand | — |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- G3H · Glyceraldehyde-3-phosphate · ligand · chains B
- G3P · Sn-glycerol-3-phosphate · ligand · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 5 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.81 | 0.89 | 45 | G3H, NDP |
| 2 | 426 | 0.80 | 0.89 | 47 | NDP, G3P |
| 3 | 399 | 0.72 | 0.83 | 41 | MRD, MPD |
| 4 | 387 | 0.72 | 0.83 | 47 | MRD |
| 5 | 165 | 0.49 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1385 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1Z82 · Crystal structure of glycerol-3-phosphate dehydrogenase (TM0378) from THERMOTOGA MARITIMA… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 1Z82 · PDBe 1Z82
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