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Structure of wild type human ferrochelatase in complex with a lead- porphyrin compound
Analyse Structure of wild type human ferrochelatase in complex with a lead- porphyrin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QD5
- 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, PP9, PB, OXY
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ferrochelatase (EC 4.99.1.1) | protein | 359 | 46% 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
- PP9 · Protoporphyrin IX · ligand · 2 copies · chains A, B
- PB · Lead (II) ion · metal · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · chains B
- ACY · Acetic acid · 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.81 | 0.84 | 82 | PB, FES, CHD, PP9, OXY, ACY |
| 2 | 138 | 0.81 | 0.98 | 35 | GOL |
| 3 | 803 | 0.80 | 0.83 | 75 | PB, FES, CHD, PP9, ACY |
| 4 | 310 | 0.60 | 0.78 | 26 | empty |
| 5 | 265 | 0.59 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1920 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2QD5 · Structure of wild type human ferrochelatase in complex with a lead-porphyrin compound · 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 2QD5 · PDBe 2QD5 · UniProt P22830
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