Research workbench
Crystal structure of a fungal catalase at 1.9 ångström
Analyse Crystal structure of a fungal catalase at 1.9 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RJR
- Type
- protein
- Length
- 2,008 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- Q6CR58
- Ligands
- HEM, NDP, K, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase (EC 1.11.1.6) | protein | 505 | 33% helix, 18% strand | Q6CR58 |
| B | Catalase (EC 1.11.1.6) | protein | 501 | 33% helix, 19% strand | Q6CR58 |
| C | Catalase (EC 1.11.1.6) | protein | 500 | 33% helix, 19% strand | Q6CR58 |
| D | Catalase (EC 1.11.1.6) | protein | 502 | 32% helix, 19% strand | Q6CR58 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 11 copies · chains A, B, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.88 | 0.92 | 49 | CL |
| 2 | 369 | 0.88 | 0.97 | 47 | empty |
| 3 | 370 | 0.87 | 0.96 | 46 | empty |
| 4 | 300 | 0.85 | 0.96 | 44 | HEM |
| 5 | 287 | 0.85 | 0.96 | 46 | HEM |
Interfaces
6 interfaces between chains.
- A–C · 4665 Ų buried · 65 hydrogen bonds · protein-protein
- B–D · 4639 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 4083 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 4057 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 2046 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6RJR · Crystal structure of a Fungal Catalase at 1.9 Angstrom · the same entry in another collection · 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 Q6CR58
- Elsewhere: RCSB PDB 6RJR · PDBe 6RJR · UniProt Q6CR58
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