Research workbench
Structure of deoxygenated hemocyanin from rapana thomasiana
Analyse Structure of deoxygenated hemocyanin from rapana thomasiana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LNL
- Type
- protein
- Length
- 1,224 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemocyanin
- UniProt
- P83040
- Ligands
- NAG, CU
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemocyanin | protein | 408 | 33% helix, 13% strand | P83040 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, C
- CU · Copper (II) ion · metal · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.75 | 0.78 | 110 | empty |
| 2 | 905 | 0.74 | 0.78 | 87 | empty |
| 3 | 263 | 0.66 | 0.83 | 37 | empty |
| 4 | 342 | 0.65 | 0.80 | 44 | empty |
| 5 | 151 | 0.52 | 0.79 | 23 | empty |
Interfaces
2 interfaces between chains.
- B–C · 338 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 326 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
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 P83040
- Elsewhere: RCSB PDB 1LNL · PDBe 1LNL · UniProt P83040
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.