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Crystal structure of human germline antibody IGHV3-53/IGKV1-39

Analyse Crystal structure of human germline antibody IGHV3-53/IGKV1-39 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I1E
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain
Ligands: SO4
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	211	6% helix, 52% strand	—
H	Fab heavy chain	protein	219	5% helix, 49% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains H
GOL · Glycerol · additive · chains L, H

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	441	0.58	0.74	54	empty
2	80	0.31	0.73	24	empty
3	66	0.30	0.74	14	empty
4	55	0.25	0.73	13	GOL

Interfaces

1 interface between chains.

L–H · 1777 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5I1E · Crystal structure of human germline antibody IGHV3-53/IGKV1-39 · the same entry in another collection · chain L against L, 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 5I1E · PDBe 5I1E

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