MolNFT v1 · #10397 · protein
Crystal structure of di-heme peroxidase from nitrosomonas europaea
1IQC: “Crystal structure of di-heme peroxidase from nitrosomonas europaea”. X-ray diffraction, 3 ligands (HEC, CA, MG), 16 pockets (best druggability 0.86). MolNFT v1 #10397 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1IQC
- Type
- protein
- Length
- 1,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Di-heme peroxidase
- UniProt
- P55929
- Ligands
- HEC, CA, MG
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Di-heme peroxidase | protein | 308 | 40% helix, 6% strand | P55929 |
Ligands and binding sites
- HEC · Heme C · ligand · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.86 | 0.91 | 77 | CA, HEC |
| 2 | 294 | 0.85 | 0.96 | 44 | HEC |
| 3 | 585 | 0.85 | 0.90 | 80 | CA, HEC |
| 4 | 310 | 0.85 | 0.95 | 44 | CA, HEC |
| 5 | 593 | 0.82 | 0.87 | 100 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2054 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 2043 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 136 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 cofactor (heme c attachment).
Compared structures
- 1IQC · Crystal structure of Di-Heme Peroxidase from Nitrosomonas europaea · the same entry in another collection · chain D against D, TM-score 1.00
- P55929 · AlphaFold monomer V2.0 prediction for cytochrome C551 peroxidase (P55929) · a predicted model of the same protein · 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 P55929
- Elsewhere: RCSB PDB 1IQC · PDBe 1IQC · UniProt P55929
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