Research workbench
Atomic resolution structure of mn catalase from thermus thermophilus
Analyse Atomic resolution structure of mn catalase from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V8U
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese-containing pseudocatalase
- EC
- 1.11.1.6
- UniProt
- Q84DB4
- Ligands
- LI, MN, O, SO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Manganese-containing pseudocatalase (EC 1.11.1.6) | protein | 302 | 52% helix, 7% strand | Q84DB4 |
Ligands and binding sites
- LI · Lithium ion · metal · 5 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- O · Oxygen atom · ion · 10 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.58 | 0.91 | 20 | empty |
| 2 | 66 | 0.54 | 0.87 | 24 | empty |
| 3 | 100 | 0.37 | 0.75 | 24 | SO4 |
| 4 | 61 | 0.30 | 0.74 | 23 | LI |
Interfaces
1 interface between chains.
- A–B · 4004 Ų buried · 74 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 2V8U · Atomic resolution structure of Mn catalase from Thermus Thermophilus · 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 Q84DB4
- Elsewhere: RCSB PDB 2V8U · PDBe 2V8U · UniProt Q84DB4
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