Research workbench
Crystal structure of isdi in complex with cobalt protoporphyrin IX
Analyse Crystal structure of isdi in complex with cobalt protoporphyrin IX in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZDP
- Type
- protein
- Length
- 220 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme-degrading monooxygenase isdi
- EC
- 1.14.99.3
- UniProt
- Q7A827
- Ligands
- COH, CL
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Heme-degrading monooxygenase isdi (EC 1.14.99.3) | protein | 110 | 21% helix, 39% strand | Q7A827 |
Ligands and binding sites
- COH · Protoporphyrin IX containing co · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.70 | 0.85 | 32 | COH, CL |
| 2 | 256 | 0.69 | 0.84 | 30 | COH, CL |
Interfaces
1 interface between chains.
- A–B · 1578 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 2ZDP · Crystal structure of IsdI in complex with Cobalt protoporphyrin IX · the same entry in another collection · chain A against A, TM-score 1.00
- Q7A827 · AlphaFold monomer V2.0 prediction for heme oxygenase (staphylobilin- producing) 2 (Q7A827) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q7A827
- Elsewhere: RCSB PDB 2ZDP · PDBe 2ZDP · UniProt Q7A827
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