MolNFT v1 · #20786 · protein
D-ribulose-5-phosphate 3-epimerase from solanum tuberosum chloroplasts
1RPX · Protein (ribulose-phosphate 3-epimerase): “D-ribulose-5-phosphate 3-epimerase from solanum tuberosum chloroplasts”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.86). MolNFT v1 #20786 on GenesisL1: 3D structure…
- PDB
- 1RPX
- Type
- protein
- Length
- 690 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (ribulose-phosphate 3-epimerase)
- EC
- 5.1.3.1
- UniProt
- Q43843
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein (ribulose-phosphate 3-epimerase) (EC 5.1.3.1) | protein | 230 | 39% helix, 19% strand | Q43843 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.86 | 0.94 | 48 | empty |
| 2 | 505 | 0.65 | 0.77 | 56 | empty |
| 3 | 179 | 0.50 | 0.77 | 25 | SO4 |
| 4 | 166 | 0.50 | 0.78 | 24 | SO4 |
| 5 | 153 | 0.49 | 0.78 | 22 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 740 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 733 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 728 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1RPX · D-ribulose-5-phosphate 3-epimerase from solanum tuberosum chloroplasts · the same entry in another collection · chain A against A, TM-score 1.00
- Q43843 · AlphaFold monomer V2.0 prediction for ribulose-phosphate 3-epimerase, chloroplastic… · 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 Q43843
- Elsewhere: RCSB PDB 1RPX · PDBe 1RPX · UniProt Q43843
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