Research workbench
Crystal structure of hrpe and D-xylulose 5-phosphate complex
Analyse Crystal structure of hrpe and D-xylulose 5-phosphate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OVR
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-phosphate 3-epimerase
- EC
- 5.1.3.1
- UniProt
- Q96AT9
- Ligands
- 5SP, FE2
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 221 | 45% helix, 20% strand | Q96AT9 |
| B | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 220 | 42% helix, 20% strand | Q96AT9 |
Ligands and binding sites
- 5SP · 5-O-phosphono-D-xylulose · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- XPE · 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.69 | 0.94 | 27 | 5SP |
| 2 | 71 | 0.66 | 0.93 | 26 | 5SP |
| 3 | 59 | 0.29 | 0.75 | 13 | empty |
| 4 | 57 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1102 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3OVR · Crystal Structure of hRPE and D-Xylulose 5-Phosphate Complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q96AT9 · AlphaFold monomer V2.0 prediction for ribulose-phosphate 3-epimerase (Q96AT9) · 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 Q96AT9
- Elsewhere: RCSB PDB 3OVR · PDBe 3OVR · UniProt Q96AT9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.