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Crystal structure of the D141E mutant of B. pseudomallei katg at pH 8.0.
Analyse Crystal structure of the D141E mutant of B. pseudomallei katg at pH 8.0. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SX2
- Type
- protein
- Length
- 1,426 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, OXY, PO4
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Catalase-peroxidase (EC 1.11.1.21) | protein | 713 | 46% helix, 8% 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 · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.85 | 0.86 | 112 | TRS |
| 2 | 514 | 0.80 | 0.87 | 70 | HEM, OXY, MPD |
| 3 | 489 | 0.80 | 0.87 | 68 | HEM, OXY, MPD |
| 4 | 88 | 0.76 | 0.98 | 19 | empty |
| 5 | 85 | 0.76 | 0.98 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3671 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5SX2 · Crystal structure of the D141E mutant of B. pseudomallei KatG at pH 8.0. · 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 5SX2 · PDBe 5SX2 · UniProt Q3JNW6
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