MolNFT v1 · #105832 · protein
Crystal structure of the methanocaldococcus jannaschii G1PDH
4RGV · Glycerol-1-phosphate dehydrogenase: “Crystal structure of the methanocaldococcus jannaschii G1PDH”. X-ray diffraction, 2 ligands (MG, ZN), 10 pockets (best druggability 0.71). MolNFT v1 #105832 on GenesisL1: 3D structure, binding…
- PDB
- 4RGV
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- 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
- MG, ZN
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 2 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 | 328 | 57% helix, 11% strand | Q58122 |
| B | Glycerol-1-phosphate dehydrogenase (EC 1.1.1.261) | protein | 333 | 54% helix, 11% strand | Q58122 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.71 | 0.83 | 40 | empty |
| 2 | 507 | 0.68 | 0.78 | 62 | empty |
| 3 | 443 | 0.67 | 0.79 | 60 | empty |
| 4 | 348 | 0.67 | 0.80 | 28 | empty |
| 5 | 284 | 0.61 | 0.79 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 1127 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4RGV · Crystal structure of the Methanocaldococcus jannaschii G1PDH · the same entry in another collection · chain A against A, 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 A 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 4RGV · PDBe 4RGV · UniProt Q58122
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