Research workbench
Structure of leishmania major peroxidase D211N mutant
Analyse Structure of leishmania major peroxidase D211N mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AMM
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ascorbate peroxidase
- EC
- 1.11.1.11, 1.11.1.5
- UniProt
- Q4Q3K2
- Ligands
- HEM, K, CA
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ascorbate peroxidase (EC 1.11.1.11, 1.11.1.5) | protein | 267 | 51% helix, 7% strand | Q4Q3K2 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.80 | 0.87 | 50 | HEM |
| 2 | 452 | 0.79 | 0.87 | 47 | HEM |
| 3 | 192 | 0.51 | 0.77 | 30 | empty |
| 4 | 66 | 0.33 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 267 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5AMM · Structure of Leishmania major peroxidase D211N mutant · 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 Q4Q3K2
- Elsewhere: RCSB PDB 5AMM · PDBe 5AMM · UniProt Q4Q3K2
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