MolNFT v1 · #134168 · protein
Crystal structure of native catalase-peroxidase katg at PH8.0
5SW4: “Crystal structure of native catalase-peroxidase katg at PH8.0”. X-ray diffraction, 4 ligands (HEM, NA, PO4), 20 pockets (best druggability 0.84). MolNFT v1 #134168 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5SW4
- 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, PO4, OXY
- Pockets
- 20 · best druggability 0.84
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
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · chains A
- 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
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.84 | 0.85 | 114 | PO4, TRS |
| 2 | 528 | 0.81 | 0.87 | 72 | HEM, MPD |
| 3 | 529 | 0.81 | 0.87 | 67 | HEM, OXY, MPD |
| 4 | 96 | 0.77 | 0.98 | 18 | empty |
| 5 | 87 | 0.77 | 0.98 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3685 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
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 5SW4 · PDBe 5SW4 · UniProt Q3JNW6
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