MolNFT v1 · #49075 · protein
F110A variant of human ferrochelatase with protoheme bound
2QD2: “F110A variant of human ferrochelatase with protoheme bound”. X-ray diffraction, 4 ligands (CHD, BCT, FES), 9 pockets (best druggability 0.80). MolNFT v1 #49075 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2QD2
- 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
- Q7KZA3
- Ligands
- CHD, BCT, FES, HEM
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ferrochelatase (EC 4.99.1.1) | protein | 359 | 49% helix, 14% strand | Q7KZA3 |
Ligands and binding sites
- CHD · Cholic acid · ligand · 4 copies · chains A, B
- BCT · Bicarbonate ion · ligand · 2 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
- IMD · Imidazole · additive · 3 copies · 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 | 122 | 0.80 | 0.98 | 35 | IMD |
| 2 | 724 | 0.79 | 0.83 | 82 | BCT, FES, IMD, CHD, HEM |
| 3 | 710 | 0.79 | 0.83 | 70 | BCT, FES, IMD, CHD, HEM |
| 4 | 254 | 0.57 | 0.78 | 26 | empty |
| 5 | 246 | 0.57 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1933 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 2QD2 · F110A variant of human ferrochelatase with protoheme bound · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7KZA3
- Elsewhere: RCSB PDB 2QD2 · PDBe 2QD2 · UniProt Q7KZA3
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