Research workbench

Cryo-EM structure of the C. elegans CLHM-1

Analyse Cryo-EM structure of the C. elegans CLHM-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LMV
Type: protein
Length: 2,223 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.6
Source: Caenorhabditis elegans
Molecule: Calcium homeostasis modulator protein
UniProt: Q18593
Pockets: 20 · best druggability 0.65

Structure

electron microscopy · resolution 3.6 · 1 distinct chain · 69% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I	Calcium homeostasis modulator protein	protein	247	69% helix, 1% strand	Q18593

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	401	0.65	0.78	34	empty
2	424	0.64	0.78	39	empty
3	350	0.64	0.79	29	empty
4	417	0.64	0.78	36	empty
5	422	0.64	0.77	35	empty

Interfaces

18 interfaces between chains.

D–E · 2708 Å² buried · 19 hydrogen bonds · protein-protein
A–I · 2702 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 2701 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 2700 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 2698 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 disulfide (disulfide).

Compared structures

6LMV · Cryo-EM structure of the C. elegans clhm-1 · the same entry in another collection · chain I against I, TM-score 1.00
Q18593 · AlphaFold monomer V2.0 prediction for calcium homeostasis modulator protein (Q18593) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 Q18593
Elsewhere: RCSB PDB 6LMV · PDBe 6LMV · UniProt Q18593

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