MolNFT v1 · #147910 · protein
Peroxidase a from dictyostelium discoideum (ddpoxa)
6ERC · Peroxinectin a: “Peroxidase a from dictyostelium discoideum (ddpoxa)”. X-ray diffraction, 6 ligands (HEM, NAG, BMA), 12 pockets (best druggability 0.83). MolNFT v1 #147910 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6ERC
- Type
- protein
- Length
- 1,022 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxinectin a
- EC
- 1.11.1.7
- UniProt
- Q6TMK4
- Ligands
- HEM, NAG, BMA, CA, NA, CL
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxinectin a (EC 1.11.1.7) | protein | 511 | 39% helix, 11% strand | Q6TMK4 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.83 | 0.85 | 71 | HEM |
| 2 | 458 | 0.80 | 0.88 | 43 | HEM |
| 3 | 313 | 0.68 | 0.83 | 38 | MRD |
| 4 | 193 | 0.60 | 0.81 | 37 | empty |
| 5 | 144 | 0.56 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 615 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan, 2 cofactor (disulfide, N-glycosylation, heme attachment, 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 Q6TMK4
- Elsewhere: RCSB PDB 6ERC · PDBe 6ERC · UniProt Q6TMK4
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