MolNFT v1 · #49077 · protein

Wild type human ferrochelatase crystallized with MNCL2

2QD4: “Wild type human ferrochelatase crystallized with MNCL2”. X-ray diffraction, 3 ligands (CHD, FES, CL), 10 pockets (best druggability 0.78). MolNFT v1 #49077 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2QD4
Type: protein
Length: 718 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferrochelatase
EC: 4.99.1.1
UniProt: P22830
Ligands: CHD, FES, CL
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ferrochelatase (EC 4.99.1.1)	protein	359	50% helix, 14% strand	P22830

Ligands and binding sites

CHD · Cholic acid · ligand · 6 copies · chains A, B
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 6 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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.78	0.99	33	GOL
2	729	0.78	0.82	83	CL, FES, CHD
3	584	0.77	0.83	56	CL, CHD
4	84	0.61	0.89	29	FES
5	242	0.57	0.79	24	CL

Interfaces

1 interface between chains.

A–B · 1901 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

2QD4 · Wild type human ferrochelatase crystallized with MnCl2 · 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 0.99

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 P22830
Elsewhere: RCSB PDB 2QD4 · PDBe 2QD4 · UniProt P22830

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