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The de novo design of an antibody combining site: crystallographic analysis of the vl domain confirms the structural model

Analyse The de novo design of an antibody combining site: crystallographic analysis of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IVL
Type: protein
Length: 214 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IgG-kappa M29B fv (light chain)
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	IgG-kappa M29B fv (light chain)	protein	107	3% helix, 50% strand	—

Ligands and binding sites

IPA · Isopropyl alcohol · additive · chains A, B

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

Pockets

3 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	167	0.52	0.79	29	empty
2	87	0.42	0.79	20	empty
3	74	0.35	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 742 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1IVL · The de novo design of an antibody combining site: crystallographic analysis of the vl… · 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 1IVL · PDBe 1IVL

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