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Crystal structure of non-cardiotoxic bence-jones light chain dimer M8

Analyse Crystal structure of non-cardiotoxic bence-jones light chain dimer M8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M6I
Type: protein
Length: 425 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain dimer
Ligands: NA
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Light chain dimer	protein	212	7% helix, 48% strand	—
A	Light chain dimer	protein	213	6% helix, 47% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	422	0.63	0.77	47	empty
2	131	0.42	0.75	30	empty
3	80	0.38	0.77	26	empty
4	69	0.30	0.74	21	empty

Interfaces

1 interface between chains.

B–A · 1241 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).

Compared structures

5M6I · Crystal structure of non-cardiotoxic Bence-Jones light chain dimer M8 · the same entry in another collection · chain B against B, 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 5M6I · PDBe 5M6I

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