Research workbench
Scorpion hemocyanin resting state pseudo atomic model built based on cryo-EM density MAP
Analyse Scorpion hemocyanin resting state pseudo atomic model built based on cryo-EM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IXV
- Type
- protein
- Length
- 7,512 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemocyanin AA6 chain
- UniProt
- P80476
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, H, I, J, K, L, M | Hemocyanin AA6 chain | protein | 626 | 36% helix, 18% strand | P80476 |
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 | 997 | 0.87 | 0.88 | 110 | empty |
| 2 | 1020 | 0.83 | 0.84 | 99 | empty |
| 3 | 542 | 0.83 | 0.89 | 61 | empty |
| 4 | 557 | 0.82 | 0.88 | 56 | empty |
| 5 | 1103 | 0.82 | 0.83 | 124 | empty |
Interfaces
26 interfaces between chains.
- D–E · 1735 Ų buried · 26 hydrogen bonds · protein-protein
- L–M · 1698 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 1676 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1645 Ų buried · 23 hydrogen bonds · protein-protein
- J–K · 1637 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3IXV · Scorpion Hemocyanin resting state pseudo atomic model built based on cryo-EM density map · the same entry in another collection · chain M against M, 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 P80476
- Elsewhere: RCSB PDB 3IXV · PDBe 3IXV · UniProt P80476
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