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Three-dimensional structure of a hybrid light chain dimer. protein engineering of a binding cavity

Analyse Three-dimensional structure of a hybrid light chain dimer. protein engineering… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1MCW
Type: protein
Length: 432 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin weir (light chain); Immunoglobulin mcg (light chain)
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
W	Immunoglobulin weir (light chain)	protein	216	8% helix, 27% strand	—
M	Immunoglobulin mcg (light chain)	protein	216	5% helix, 39% strand	—

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	571	0.69	0.78	64	empty
2	395	0.66	0.79	54	empty
3	101	0.50	0.82	25	empty
4	148	0.43	0.75	25	empty
5	58	0.33	0.77	15	empty

Interfaces

1 interface between chains.

W–M · 1728 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 modified (disulfide, cyclization).

Compared structures

1MCW · Three-dimensional structure of a hybrid light chain dimer. protein engineering of a… · the same entry in another collection · chain W against W, 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 1MCW · PDBe 1MCW

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