Research workbench

Complex between CD19 (N138Q mutant) and B43 Fab

Analyse Complex between CD19 (N138Q mutant) and B43 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AL5
Type: protein
Length: 673 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-lymphocyte antigen CD19; B43 light chain; B43 heavy chain
UniProt: P15391, Q6P5S8, A8K008
Ligands: NAG
Pockets: 6 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	B-lymphocyte antigen CD19	protein	234	3% helix, 45% strand	P15391
L	B43 light chain	protein	217	6% helix, 51% strand	Q6P5S8
H	B43 heavy chain	protein	222	7% helix, 52% strand	A8K008

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A

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

Pockets

6 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	312	0.57	0.76	32	empty
2	271	0.51	0.75	39	empty
3	151	0.44	0.75	32	empty
4	71	0.30	0.74	18	empty
5	68	0.30	0.74	16	empty

Interfaces

3 interfaces between chains.

L–H · 1869 Å² buried · 16 hydrogen bonds · protein-protein
A–H · 720 Å² buried · 11 hydrogen bonds · protein-protein
A–L · 109 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, cyclization).

Compared structures

6AL5 · Complex between CD19 (N138Q mutant) and B43 Fab · the same entry in another collection · chain A against A, TM-score 1.00
P15391 · AlphaFold monomer V2.0 prediction for B-lymphocyte antigen CD19 (P15391) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P15391
Every structure of UniProt Q6P5S8
Every structure of UniProt A8K008
Elsewhere: RCSB PDB 6AL5 · PDBe 6AL5 · UniProt P15391 · UniProt Q6P5S8 · UniProt A8K008

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