Research workbench
0.93 a structure of manganese-bound manganese peroxidase
Analyse 0.93 a structure of manganese-bound manganese peroxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M5Q
- Type
- protein
- Length
- 357 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese peroxidase 1
- EC
- 1.11.1.13
- UniProt
- Q02567
- Ligands
- HEM, NAG, MAN, CA, MN
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Manganese peroxidase 1 (EC 1.11.1.13) | protein | 357 | 39% helix, 6% strand | Q02567 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.80 | 0.89 | 43 | MN, HEM |
| 2 | 210 | 0.50 | 0.76 | 35 | empty |
| 3 | 89 | 0.41 | 0.78 | 22 | empty |
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation, O-glycosylation).
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 Q02567
- Elsewhere: RCSB PDB 3M5Q · PDBe 3M5Q · UniProt Q02567
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