MolNFT v1 · #49076 · protein
Wild type human ferrochelatase crystallized with ammonium sulfate
2QD3: “Wild type human ferrochelatase crystallized with ammonium sulfate”. X-ray diffraction, 3 ligands (CHD, FES, HEM), 7 pockets (best druggability 0.81). MolNFT v1 #49076 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2QD3
- 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, HEM
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ferrochelatase (EC 4.99.1.1) | protein | 359 | 51% helix, 14% strand | P22830 |
Ligands and binding sites
- CHD · Cholic acid · ligand · 5 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · chains B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.81 | 0.84 | 78 | FES, HEM |
| 2 | 128 | 0.81 | 0.98 | 33 | GOL |
| 3 | 842 | 0.79 | 0.82 | 80 | FES, CHD |
| 4 | 255 | 0.58 | 0.79 | 25 | empty |
| 5 | 280 | 0.57 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1947 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2QD3 · Wild type human ferrochelatase crystallized with ammonium sulfate · 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 2QD3 · PDBe 2QD3 · UniProt P22830
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