MolNFT v1 · #155479 · protein
High resolution crystal structure of crustacean hemocyanin.
6L8S: “High resolution crystal structure of crustacean hemocyanin.”. X-ray diffraction, 6 ligands (NAG, CU, MG), 20 pockets (best druggability 0.82). MolNFT v1 #155479 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6L8S
- Type
- protein
- Length
- 1,950 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemocyanin
- Ligands
- NAG, CU, MG, O, SO4, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemocyanin | protein | 650 | 39% helix, 18% strand | — |
| B | Hemocyanin | protein | 650 | 39% helix, 18% strand | — |
| C | Hemocyanin | protein | 650 | 39% helix, 18% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C
- MG · Magnesium ion · metal · 5 copies · chains A, B, C
- O · Oxygen atom · ion · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.82 | 0.85 | 92 | EDO |
| 2 | 116 | 0.81 | 0.98 | 24 | empty |
| 3 | 122 | 0.80 | 0.98 | 26 | empty |
| 4 | 117 | 0.80 | 0.98 | 25 | empty |
| 5 | 434 | 0.68 | 0.80 | 55 | EDO |
Interfaces
3 interfaces between chains.
- B–C · 706 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 705 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 692 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6L8S · High resolution crystal structure of crustacean hemocyanin. · 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
- Elsewhere: RCSB PDB 6L8S · PDBe 6L8S
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