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Crystal structure of non-amyloidogenic light chain dimer M7

Analyse Crystal structure of non-amyloidogenic light chain dimer M7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MVG
Type: protein
Length: 386 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Homo sapiens
Molecule: light chain dimer
Pockets: 6 · best druggability 0.65

Structure

x-ray diffraction · resolution 2.2 · 2 distinct chains · 8% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	light chain dimer	protein	177	8% helix, 45% strand	—
B	light chain dimer	protein	209	9% helix, 48% strand	—

Ligands and binding sites

GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	249	0.65	0.82	25	empty
2	368	0.56	0.74	54	empty
3	65	0.55	0.87	15	empty
4	146	0.43	0.75	22	empty
5	162	0.43	0.74	38	empty

Interfaces

1 interface between chains.

A–B · 1455 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5MVG · Crystal structure of non-amyloidogenic light chain dimer M7 · 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 5MVG · PDBe 5MVG

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