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Scorpion hemocyanin activated state pseudo atomic model built based on cryo-EM density MAP

Analyse Scorpion hemocyanin activated 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: 3IXW
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 0.89

Structure

electron microscopy · 1 distinct chain · 33% helix, 17% 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	33% helix, 17% strand	P80476

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1172	0.89	0.90	138	empty
2	1106	0.88	0.90	147	empty
3	1047	0.88	0.90	145	empty
4	812	0.87	0.90	106	empty
5	1054	0.86	0.87	110	empty

Interfaces

26 interfaces between chains.

J–K · 1675 Å² buried · 18 hydrogen bonds · protein-protein
L–M · 1497 Å² buried · 17 hydrogen bonds · protein-protein
F–G · 1456 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 1315 Å² buried · 10 hydrogen bonds · protein-protein
H–I · 1240 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3IXW · Scorpion Hemocyanin activated 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 3IXW · PDBe 3IXW · UniProt P80476

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