MolNFT v1 · #92631 · protein
Crystal structure of the leishmania major peroxidase-cytochrome C complex
4GED · Ascorbate peroxidase: “Crystal structure of the leishmania major peroxidase-cytochrome C complex”. X-ray diffraction, 4 ligands (HEM, HEC, K), 5 pockets (best druggability 0.80). MolNFT v1 #92631 on GenesisL1: 3D structure, binding…
- PDB
- 4GED
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ascorbate peroxidase; Cytochrome C
- EC
- 1.11.1.11
- UniProt
- Q4Q3K2, Q4QEN5
- Ligands
- HEM, HEC, K, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ascorbate peroxidase (EC 1.11.1.11) | protein | 268 | 51% helix, 7% strand | Q4Q3K2 |
| B | Cytochrome C | protein | 102 | 40% helix, 2% strand | Q4QEN5 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- HEC · Heme C · ligand · chains A, B
- K · Potassium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.80 | 0.87 | 49 | HEM |
| 2 | 292 | 0.77 | 0.89 | 43 | HEC |
| 3 | 52 | 0.37 | 0.80 | 16 | empty |
| 4 | 96 | 0.37 | 0.76 | 25 | empty |
| 5 | 75 | 0.33 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 637 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (heme c attachment).
Compared structures
- 4GED · Crystal Structure of the Leishmania Major Peroxidase-Cytochrome C Complex · 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
- Every structure of UniProt Q4QEN5
- Elsewhere: RCSB PDB 4GED · PDBe 4GED · UniProt Q4Q3K2 · UniProt Q4QEN5
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