Research workbench
Crystal structure of katb, a manganese catalase from anabaena PCC7120
Analyse Crystal structure of katb, a manganese catalase from anabaena PCC7120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R42
- Type
- protein
- Length
- 658 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALR3090 protein
- UniProt
- Q8YSJ5
- Ligands
- MN, CA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALR3090 protein | protein | 219 | 52% helix, 5% strand | Q8YSJ5 |
| B | ALR3090 protein | protein | 219 | 51% helix, 5% strand | Q8YSJ5 |
| C | ALR3090 protein | protein | 220 | 51% helix, 4% strand | Q8YSJ5 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C
- CA · Calcium ion · metal · 5 copies · chains A, C, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
- P6G · Hexaethylene glycol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.79 | 0.88 | 78 | empty |
| 2 | 171 | 0.45 | 0.75 | 29 | empty |
| 3 | 144 | 0.45 | 0.77 | 24 | P6G |
| 4 | 147 | 0.40 | 0.73 | 19 | empty |
| 5 | 60 | 0.28 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3036 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1947 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 702 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4R42 · Crystal structure of KatB, a manganese catalase from Anabaena PCC7120 · 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 Q8YSJ5
- Elsewhere: RCSB PDB 4R42 · PDBe 4R42 · UniProt Q8YSJ5
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