MolNFT v1 · #78551 · protein

FE(II)-hppe with R-hpp

3SCG · Epoxidase: “FE(II)-hppe with R-hpp”. X-ray diffraction, 2 ligands (TB6, FE2), 6 pockets (best druggability 0.61). MolNFT v1 #78551 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SCG
Type: protein
Length: 579 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epoxidase
UniProt: Q56185
Ligands: TB6, FE2
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Epoxidase	protein	193	28% helix, 32% strand	Q56185

Ligands and binding sites

TB6 · [(2R)-2-hydroxypropyl]phosphonic acid · ligand · 3 copies · chains A, B, C
FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	383	0.61	0.77	34	empty
2	267	0.61	0.80	35	TB6, FE2
3	225	0.59	0.80	30	TB6, FE2
4	69	0.47	0.83	16	TB6, FE2
5	164	0.45	0.75	29	empty

Interfaces

3 interfaces between chains.

A–B · 1513 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 184 Å² buried · 1 hydrogen bond · protein-protein
B–C · 50 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3SCG · Fe(II)-HppE with R-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 0.91

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 3SCG · PDBe 3SCG · UniProt Q56185

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