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Structural basis for the binding of monoclonal antibody 5D2 to the tryptophan-rich lipid-binding loop in lipoprotein lipase

Analyse Structural basis for the binding of monoclonal antibody 5D2 to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WT3
Type: protein
Length: 428 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5D2 Fab heavy chain; 5D2 Fab light chain
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	5D2 Fab heavy chain	protein	216	3% helix, 50% strand	—
L	5D2 Fab light chain	protein	212	6% helix, 46% strand	—

Pockets

5 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	297	0.57	0.77	39	empty
2	140	0.38	0.73	24	empty
3	89	0.36	0.74	14	empty
4	76	0.32	0.74	21	empty
5	71	0.28	0.73	19	empty

Interfaces

1 interface between chains.

H–L · 1967 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6WT3 · Structural basis for the binding of monoclonal antibody 5D2 to the tryptophan-rich… · the same entry in another collection · chain H against H, 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 6WT3 · PDBe 6WT3

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