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Crystal structure of hexameric haemocyanin from panulirus interruptus refined at 3.2 ångströms resolution
Analyse Crystal structure of hexameric haemocyanin from panulirus interruptus refined… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HCY
- Type
- protein
- Length
- 3,864 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arthropodan hemocyanin
- UniProt
- P04254
- Ligands
- NAG, CU
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Arthropodan hemocyanin | protein | 644 | 33% helix, 15% strand | P04254 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F
- CU · Copper (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.83 | 0.98 | 28 | empty |
| 2 | 169 | 0.82 | 0.97 | 28 | empty |
| 3 | 174 | 0.82 | 0.97 | 28 | empty |
| 4 | 169 | 0.82 | 0.97 | 27 | empty |
| 5 | 1187 | 0.82 | 0.83 | 119 | empty |
Interfaces
12 interfaces between chains.
- D–E · 1457 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 1441 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1412 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 603 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 603 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 1HCY · Crystal structure of hexameric haemocyanin from panulirus interruptus refined at 3.2… · the same entry in another collection · chain C against C, TM-score 1.00
- P04254 · AlphaFold monomer V2.0 prediction for hemocyanin a chain (P04254) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P04254
- Elsewhere: RCSB PDB 1HCY · PDBe 1HCY · UniProt P04254
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