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Crystal structure of G1PDH with NADPH from methanocaldococcus jannaschii
Analyse Crystal structure of G1PDH with NADPH from methanocaldococcus jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RFL
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-1-phosphate dehydrogenase [NAD(P)+]
- EC
- 1.1.1.261
- UniProt
- Q58122
- Ligands
- NDP, K, ZN, NA
- Pockets
- 18 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycerol-1-phosphate dehydrogenase [NAD(P)+] (EC 1.1.1.261) | protein | 332 | 56% helix, 11% strand | Q58122 |
| C | Glycerol-1-phosphate dehydrogenase [NAD(P)+] (EC 1.1.1.261) | protein | 329 | 55% helix, 11% strand | Q58122 |
| D | Glycerol-1-phosphate dehydrogenase [NAD(P)+] (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
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains C, D
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.69 | 0.81 | 37 | EDO |
| 2 | 525 | 0.68 | 0.79 | 59 | NDP |
| 3 | 514 | 0.68 | 0.79 | 52 | NDP, EDO |
| 4 | 381 | 0.68 | 0.80 | 34 | EDO |
| 5 | 513 | 0.67 | 0.78 | 57 | NDP |
Interfaces
2 interfaces between chains.
- A–B · 1171 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1111 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4RFL · Crystal structure of G1PDH with NADPH from Methanocaldococcus jannaschii · 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 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 4RFL · PDBe 4RFL · UniProt Q58122
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