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Crystal structure of cardiotoxic bence-jones light chain dimer H10

Analyse Crystal structure of cardiotoxic bence-jones light chain dimer H10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M76
Type: protein
Length: 422 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain dimer
Ligands: BR
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Light chain dimer	protein	211	7% helix, 50% strand	—

Ligands and binding sites

BR · Bromide ion · ion · chains B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	192	0.71	0.88	30	empty
2	724	0.68	0.76	67	empty
3	131	0.39	0.74	26	empty
4	62	0.31	0.75	24	empty
5	64	0.30	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 1751 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5M76 · Crystal structure of cardiotoxic Bence-Jones light chain dimer H10 · 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 5M76 · PDBe 5M76

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