MolNFT v1 · #115430 · protein
Crystal structure of eukaryotic oxoiron MAGKATG2 at pH 8.5
5CJH · Catalase-peroxidase 2: “Crystal structure of eukaryotic oxoiron MAGKATG2 at pH 8.5”. X-ray diffraction, 2 ligands (522, OH), 20 pockets (best druggability 0.87). MolNFT v1 #115430 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5CJH
- Type
- protein
- Length
- 1,467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase-peroxidase 2
- EC
- 1.11.1.21
- UniProt
- A4QUT2
- Ligands
- 522, OH
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase-peroxidase 2 (EC 1.11.1.21) | protein | 734 | 44% helix, 8% strand | A4QUT2 |
| B | Catalase-peroxidase 2 (EC 1.11.1.21) | protein | 733 | 44% helix, 7% strand | A4QUT2 |
Ligands and binding sites
- 522 · Peroxidized heme · ligand · 2 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.87 | 0.92 | 72 | empty |
| 2 | 614 | 0.82 | 0.87 | 73 | 522, OH |
| 3 | 546 | 0.81 | 0.87 | 69 | 522, OH |
| 4 | 819 | 0.75 | 0.79 | 86 | empty |
| 5 | 77 | 0.74 | 0.98 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 4995 Ų buried · 75 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- A4QUT2 · AlphaFold monomer V2.0 prediction for catalase-peroxidase 2 (A4QUT2) · a predicted model of the same protein · chain A 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 A4QUT2
- Elsewhere: RCSB PDB 5CJH · PDBe 5CJH · UniProt A4QUT2
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