Research workbench
Crystal structure of FE(II)-hppe with alternative substrate (R)-1-hpp
Analyse Crystal structure of FE(II)-hppe with alternative substrate (R)-1-hpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J1W
- Type
- protein
- Length
- 582 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxidase
- UniProt
- Q56185
- Ligands
- FFQ, FE2
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Epoxidase | protein | 194 | 26% helix, 28% strand | Q56185 |
Ligands and binding sites
- FFQ · [(1R)-1-hydroxypropyl]phosphonic acid · ligand · 3 copies · chains A, B, C
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.63 | 0.77 | 33 | empty |
| 2 | 251 | 0.59 | 0.79 | 37 | FE2, FFQ |
| 3 | 269 | 0.59 | 0.78 | 34 | FE2, FFQ |
| 4 | 80 | 0.49 | 0.82 | 15 | FE2, FFQ |
| 5 | 140 | 0.46 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1531 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 186 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4J1W · Crystal Structure of Fe(II)-HppE with alternative substrate (R)-1-HPP · the same entry in another collection · chain A against A, TM-score 1.00
- Q56185 · AlphaFold monomer V2.0 prediction for (S)-2-hydroxypropylphosphonic acid epoxidase… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q56185
- Elsewhere: RCSB PDB 4J1W · PDBe 4J1W · UniProt Q56185
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