MolNFT v1 · #83525 · protein
Crystal structure of hemolymph type prophenoloxidase (propob) from crustacean
3WKY · Prophenoloxidase B: “Crystal structure of hemolymph type prophenoloxidase (propob) from crustacean”. X-ray diffraction, 5 ligands (CUO, NAG, NA), 20 pockets (best druggability 0.72). MolNFT v1 #83525 on GenesisL1: 3D structure…
- PDB
- 3WKY
- Type
- protein
- Length
- 1,310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prophenoloxidase B
- UniProt
- G5EKM4
- Ligands
- CUO, NAG, NA, MG, CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prophenoloxidase B | protein | 655 | 36% helix, 18% strand | G5EKM4 |
| B | Prophenoloxidase B | protein | 655 | 36% helix, 18% strand | G5EKM4 |
Ligands and binding sites
- CUO · CU2-O2 cluster · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- NA · Sodium ion · metal · chains A
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.72 | 0.76 | 109 | EDO |
| 2 | 89 | 0.67 | 0.92 | 27 | empty |
| 3 | 86 | 0.66 | 0.92 | 26 | empty |
| 4 | 222 | 0.63 | 0.83 | 32 | empty |
| 5 | 209 | 0.60 | 0.81 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 593 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 3WKY · Crystal structure of hemolymph type prophenoloxidase (proPOb) from crustacean · 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 G5EKM4
- Elsewhere: RCSB PDB 3WKY · PDBe 3WKY · UniProt G5EKM4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.