MolNFT v1 · #78550 · protein

FE(II)-hppe with S-hpp and no

3SCF · Epoxidase: “FE(II)-hppe with S-hpp and no”. X-ray diffraction, 3 ligands (S0H, FE2, NO), 7 pockets (best druggability 0.62). MolNFT v1 #78550 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SCF
Type: protein
Length: 579 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epoxidase
UniProt: Q56185
Ligands: S0H, FE2, NO
Pockets: 7 · best druggability 0.62

Structure

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

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

Ligands and binding sites

S0H · (S)-2-hydroxypropylphosphonic acid · ligand · 3 copies · chains A, B, C
FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
NO · Nitric oxide · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.62	0.77	37	empty
2	285	0.62	0.80	35	FE2, NO, S0H
3	261	0.60	0.80	32	FE2, NO, S0H
4	76	0.50	0.83	14	FE2, S0H
5	119	0.42	0.76	18	empty

Interfaces

3 interfaces between chains.

A–B · 1577 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 187 Å² buried · 1 hydrogen bond · protein-protein
B–C · 51 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3SCF · Fe(II)-HppE with S-HPP and NO · 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 3SCF · PDBe 3SCF · UniProt Q56185

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