Research workbench
Crystal structure of ferrochelatase from the yeast, saccharomyces cerevisiae, with COBALT(II) as the substrate ion
Analyse Crystal structure of ferrochelatase from the yeast, saccharomyces cerevisiae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L8X
- Type
- protein
- Length
- 709 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferrochelatase
- EC
- 4.99.1.1
- UniProt
- P16622
- Ligands
- CO
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferrochelatase (EC 4.99.1.1) | protein | 355 | 46% helix, 14% strand | P16622 |
| B | Ferrochelatase (EC 4.99.1.1) | protein | 354 | 47% helix, 14% strand | P16622 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 2 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 | 155 | 0.82 | 0.98 | 38 | empty |
| 2 | 393 | 0.82 | 0.90 | 54 | CO |
| 3 | 720 | 0.78 | 0.82 | 53 | CO |
| 4 | 303 | 0.59 | 0.78 | 26 | empty |
| 5 | 287 | 0.54 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1477 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1L8X · Crystal Structure of Ferrochelatase from the Yeast, Saccharomyces cerevisiae, with… · the same entry in another collection · chain A against A, TM-score 1.00
- P16622 · AlphaFold monomer V2.0 prediction for ferrochelatase, mitochondrial (P16622) · a predicted model of the same protein · chain B 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 P16622
- Elsewhere: RCSB PDB 1L8X · PDBe 1L8X · UniProt P16622
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