Research workbench
Crystal structure of the methanocaldococcus jannaschii G1PDH with NADPH and dhap
Analyse Crystal structure of the methanocaldococcus jannaschii G1PDH with NADPH and dhap in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RGQ
- Type
- protein
- Length
- 1,326 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-1-phosphate dehydrogenase
- EC
- 1.1.1.261
- UniProt
- Q58122
- Ligands
- NDP, 13P, 1GP, K, ZN
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol-1-phosphate dehydrogenase (EC 1.1.1.261) | protein | 332 | 56% helix, 11% strand | Q58122 |
| B | Glycerol-1-phosphate dehydrogenase (EC 1.1.1.261) | protein | 333 | 55% helix, 11% strand | Q58122 |
| C | Glycerol-1-phosphate dehydrogenase (EC 1.1.1.261) | protein | 330 | 55% helix, 11% strand | Q58122 |
| D | Glycerol-1-phosphate dehydrogenase (EC 1.1.1.261) | protein | 331 | 56% helix, 11% strand | Q58122 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 3 copies · chains A, C, D
- 1GP · Sn-glycerol-1-phosphate · ligand · chains B
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.68 | 0.81 | 40 | empty |
| 2 | 476 | 0.68 | 0.79 | 57 | NDP, 13P |
| 3 | 540 | 0.68 | 0.78 | 55 | NDP, 13P |
| 4 | 452 | 0.67 | 0.79 | 55 | NDP, 13P |
| 5 | 333 | 0.67 | 0.81 | 34 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1273 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1227 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4RGQ · Crystal structure of the Methanocaldococcus jannaschii G1PDH with NADPH and DHAP · the same entry in another collection · chain D against D, TM-score 1.00
- Q58122 · AlphaFold monomer V2.0 prediction for glycerol-1-phosphate dehydrogenase [NAD(P)+]… · a predicted model of the same protein · chain D 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 Q58122
- Elsewhere: RCSB PDB 4RGQ · PDBe 4RGQ · UniProt Q58122
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