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Crystal structure of LI33 IGG1 Fab

Analyse Crystal structure of LI33 IGG1 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KYK
Type: protein
Length: 431 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain LI33 IGG1; Light chain LI33 IGG1
Ligands: SO4
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Heavy chain LI33 IGG1	protein	220	6% helix, 43% strand	—
L	Light chain LI33 IGG1	protein	211	5% helix, 48% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains H, L

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	468	0.57	0.73	46	empty
2	74	0.30	0.73	20	empty
3	62	0.29	0.74	15	empty
4	55	0.28	0.75	17	SO4

Interfaces

1 interface between chains.

H–L · 1814 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3KYK · Crystal structure of li33 Igg1 Fab · 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 3KYK · PDBe 3KYK

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