MolNFT v1 · #124817 · protein
Crystal structure of the L326D variant of catalase-peroxidase from B. pseudomallei
5KQI: “Crystal structure of the L326D variant of catalase-peroxidase from B. pseudomallei”. X-ray diffraction, 5 ligands (HEM, NA, CL), 20 pockets (best druggability 0.86). MolNFT v1 #124817 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KQI
- Type
- protein
- Length
- 1,428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase-peroxidase
- EC
- 1.11.1.21
- UniProt
- Q3JNW6
- Ligands
- HEM, NA, CL, OXY, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Catalase-peroxidase (EC 1.11.1.21) | protein | 714 | 46% 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
- CL · Chloride ion · ion · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- 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 | 1023 | 0.86 | 0.87 | 119 | empty |
| 2 | 536 | 0.81 | 0.87 | 66 | HEM, OXY, MPD |
| 3 | 540 | 0.80 | 0.86 | 70 | HEM, OXY, MPD |
| 4 | 94 | 0.78 | 0.98 | 20 | empty |
| 5 | 89 | 0.76 | 0.98 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3829 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5KQI · Crystal structure of the L326D 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 5KQI · PDBe 5KQI · UniProt Q3JNW6
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