MolNFT v1 · #4211 · protein
Human erythrocyte catalase 3-amino-1,2,4-triazole complex
1DGH · Protein (catalase): “Human erythrocyte catalase 3-amino-1,2,4-triazole complex”. X-ray diffraction, 2 ligands (HEM, NDP), 20 pockets (best druggability 0.88). MolNFT v1 #4211 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1DGH
- Type
- protein
- Length
- 1,991 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (catalase)
- EC
- 1.11.1.6
- UniProt
- P04040
- Ligands
- HEM, NDP
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (catalase) (EC 1.11.1.6) | protein | 497 | 34% helix, 19% strand | P04040 |
| B, D | Protein (catalase) (EC 1.11.1.6) | protein | 498 | 33% helix, 18% strand | P04040 |
| C | Protein (catalase) (EC 1.11.1.6) | protein | 498 | 33% helix, 18% strand | P04040 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, B, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, C
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 | 419 | 0.88 | 0.96 | 52 | empty |
| 2 | 678 | 0.88 | 0.92 | 52 | empty |
| 3 | 404 | 0.87 | 0.95 | 51 | empty |
| 4 | 264 | 0.85 | 0.96 | 46 | HEM |
| 5 | 271 | 0.85 | 0.96 | 45 | HEM |
Interfaces
6 interfaces between chains.
- B–D · 4966 Ų buried · 81 hydrogen bonds · protein-protein
- A–C · 4950 Ų buried · 79 hydrogen bonds · protein-protein
- C–D · 4709 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 4699 Ų buried · 55 hydrogen bonds · protein-protein
- A–D · 2104 Ų buried · 34 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 P04040
- Elsewhere: RCSB PDB 1DGH · PDBe 1DGH · UniProt P04040
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.