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Hg and protoporphyrin bound human ferrochelatase

Analyse Hg and protoporphyrin bound human ferrochelatase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HCN
Type: protein
Length: 718 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferrochelatase, mitochondrial
EC: 4.99.1.1
UniProt: P22830
Ligands: CHD, FES, HEM, BCT, SO4
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ferrochelatase, mitochondrial (EC 4.99.1.1)	protein	359	49% helix, 14% strand	P22830

Ligands and binding sites

CHD · Cholic acid · ligand · 4 copies · chains A, B
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
BCT · Bicarbonate ion · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A, B
IMD · Imidazole · additive · 3 copies · chains A, B
GOL · Glycerol · additive · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	735	0.81	0.84	80	FES, CHD, IMD, HEM
2	811	0.81	0.83	78	FES, CHD, IMD, BCT, HEM
3	115	0.79	0.98	34	GOL
4	281	0.59	0.78	26	empty
5	215	0.54	0.78	26	empty

Interfaces

1 interface between chains.

A–B · 1908 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

3HCN · Hg and protoporphyrin bound Human Ferrochelatase · the same entry in another collection · chain A against A, TM-score 1.00
P22830 · AlphaFold monomer V2.0 prediction for ferrochelatase, mitochondrial (P22830) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P22830
Elsewhere: RCSB PDB 3HCN · PDBe 3HCN · UniProt P22830

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