Research workbench
Crystal structure of the V293D variant of catalase-peroxidase from B. pseudomallei
Analyse Crystal structure of the V293D variant of catalase-peroxidase from B.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KQH
- Type
- protein
- Length
- 1,426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.82
- Source
- Burkholderia pseudomallei (strain 1710b)
- Molecule
- Catalase-peroxidase
- EC
- 1.11.1.21
- UniProt
- Q3JNW6
- Ligands
- HEM, NA, OXY, PO4, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.82 · 1 distinct chain · 47% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Catalase-peroxidase (EC 1.11.1.21) | protein | 713 | 47% helix, 7% strand | Q3JNW6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.84 | 0.85 | 108 | empty |
| 2 | 514 | 0.82 | 0.88 | 67 | HEM, OXY, MPD |
| 3 | 525 | 0.81 | 0.87 | 70 | HEM, OXY, MPD |
| 4 | 91 | 0.78 | 0.99 | 18 | empty |
| 5 | 86 | 0.76 | 0.98 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3677 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5KQH · Crystal structure of the V293D variant of catalase-peroxidase from B. pseudomallei · the same entry in another collection · chain A against A, TM-score 1.00
- Q3JNW6 · AlphaFold monomer V2.0 prediction for catalase-peroxidase (Q3JNW6) · 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 Q3JNW6
- Elsewhere: RCSB PDB 5KQH · PDBe 5KQH · UniProt Q3JNW6
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