Research workbench
Keyhole limpet hemocyanin (klh): 9A cryoem structure and molecular model of the KLH1 didecamer reveal the interfaces and intricate topology of the 160 functional units
Analyse Keyhole limpet hemocyanin (klh): 9A cryoem structure and molecular model of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BED
- Type
- protein
- Length
- 6,796 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemocyanin KLH1
- UniProt
- Q53IP9
- Ligands
- CUO
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 34% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemocyanin KLH1 | protein | 1664 | 35% helix, 14% strand | Q53IP9 |
| B, D | Hemocyanin KLH1 | protein | 1734 | 33% helix, 13% strand | Q53IP9 |
Ligands and binding sites
- CUO · CU2-O2 cluster · ligand · 16 copies · chains A, B, C, D
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 | 1097 | 0.83 | 0.84 | 135 | empty |
| 2 | 1151 | 0.83 | 0.84 | 138 | empty |
| 3 | 966 | 0.82 | 0.83 | 127 | empty |
| 4 | 894 | 0.81 | 0.83 | 107 | empty |
| 5 | 855 | 0.81 | 0.83 | 95 | empty |
Interfaces
3 interfaces between chains.
- B–D · 3018 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2776 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2414 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide (disulfide).
Compared structures
- 4BED · Keyhole limpet hemocyanin (KLH): 9A cryoEM structure and molecular model of the KLH1… · 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 Q53IP9
- Elsewhere: RCSB PDB 4BED · PDBe 4BED · UniProt Q53IP9
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