MolNFT v1 · #160500 · protein
The structure of the triclinic crystal form of beef liver catalase at 1.85 a resolution
6PM7: “The structure of the triclinic crystal form of beef liver catalase at 1.85 a resolution”. X-ray diffraction, 2 ligands (HEM, NDP), 15 pockets (best druggability 0.85). MolNFT v1 #160500 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6PM7
- Type
- protein
- Length
- 996 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- P00432
- Ligands
- HEM, NDP
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Catalase (EC 1.11.1.6) | protein | 498 | 34% helix, 17% strand | P00432 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.85 | 0.96 | 43 | HEM |
| 2 | 244 | 0.84 | 0.96 | 37 | HEM |
| 3 | 1180 | 0.80 | 0.81 | 83 | empty |
| 4 | 809 | 0.77 | 0.80 | 76 | empty |
| 5 | 265 | 0.63 | 0.81 | 39 | NDP |
Interfaces
1 interface between chains.
- A–B · 4952 Ų buried · 74 hydrogen bonds · protein-protein
Compared structures
- 6PM7 · The structure of the triclinic crystal form of beef liver catalase at 1.85 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P00432 · AlphaFold monomer V2.0 prediction for catalase (P00432) · a predicted model of the same protein · chain B 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 P00432
- Elsewhere: RCSB PDB 6PM7 · PDBe 6PM7 · UniProt P00432
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