MolNFT v2 · #224574 · protein
Human erythrocyte catalase
8WZJ: “Human erythrocyte catalase”. Electron microscopy at 2.7, 2 ligands (HEM, NDP), 20 pockets (best druggability 0.88). MolNFT v2 #224574 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8WZJ
- Type
- protein
- Length
- 1,988 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- P04040
- Ligands
- HEM, NDP
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 2.7 · 1 distinct chain · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Catalase (EC 1.11.1.6) | protein | 497 | 33% helix, 19% strand | P04040 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains B, D, A, C
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.88 | 0.92 | 52 | empty |
| 2 | 383 | 0.87 | 0.96 | 56 | empty |
| 3 | 385 | 0.87 | 0.96 | 57 | empty |
| 4 | 270 | 0.85 | 0.96 | 37 | HEM |
| 5 | 266 | 0.84 | 0.96 | 41 | HEM |
Interfaces
6 interfaces between chains.
- B–D · 5071 Ų buried · 82 hydrogen bonds · protein-protein
- A–C · 5065 Ų buried · 81 hydrogen bonds · protein-protein
- B–A · 4673 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 4673 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 2041 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- P04040 · AlphaFold monomer V2.0 prediction for catalase (P04040) · 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 P04040
- Elsewhere: RCSB PDB 8WZJ · PDBe 8WZJ · UniProt P04040
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