Research workbench
Crystal structure of catalase-peroxidase from haloarcula marismortui
Analyse Crystal structure of catalase-peroxidase from haloarcula marismortui in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ITK
- Type
- protein
- Length
- 1,421 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase-peroxidase
- EC
- 1.11.1.6
- UniProt
- O59651
- Ligands
- HEM, CL, SO4, UNX
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase-peroxidase (EC 1.11.1.6) | protein | 707 | 46% helix, 8% strand | O59651 |
| B | Catalase-peroxidase (EC 1.11.1.6) | protein | 714 | 46% helix, 7% strand | O59651 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 16 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- UNX · Unknown atom or ion · ion · 6 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.83 | 0.86 | 98 | CL |
| 2 | 611 | 0.83 | 0.87 | 69 | UNX, HEM |
| 3 | 593 | 0.82 | 0.87 | 66 | CL, HEM |
| 4 | 784 | 0.81 | 0.84 | 99 | SO4, CL |
| 5 | 579 | 0.79 | 0.85 | 80 | SO4, CL |
Interfaces
1 interface between chains.
- A–B · 3775 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 1ITK · Crystal structure of catalase-peroxidase from Haloarcula marismortui · the same entry in another collection · chain A against A, TM-score 1.00
- O59651 · AlphaFold monomer V2.0 prediction for catalase-peroxidase 2 (O59651) · 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 O59651
- Elsewhere: RCSB PDB 1ITK · PDBe 1ITK · UniProt O59651
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