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Structure of full-length CD20 in complex with obinutuzumab Fab

Analyse Structure of full-length CD20 in complex with obinutuzumab Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Y9A
Type: protein
Length: 775 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-lymphocyte antigen CD20; Obinutuzumab Fab heavy chain; Obinutuzumab Fab light chain
UniProt: P11836
Pockets: 19 · best druggability 0.77

Structure

electron microscopy · 3 distinct chains · 23% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	B-lymphocyte antigen CD20	protein	169	70% helix, 0% strand	P11836
H	Obinutuzumab Fab heavy chain	protein	218	6% helix, 43% strand	—
L	Obinutuzumab Fab light chain	protein	219	5% helix, 45% strand	—

Pockets

19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	954	0.77	0.79	76	empty
2	169	0.74	0.91	40	empty
3	179	0.73	0.89	36	empty
4	129	0.72	0.91	37	empty
5	302	0.72	0.85	42	empty

Interfaces

5 interfaces between chains.

H–L · 1821 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1366 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 331 Å² buried · 4 hydrogen bonds · protein-protein
B–H · 272 Å² buried · 3 hydrogen bonds · protein-protein
A–L · 238 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6Y9A · Structure of full-length CD20 in complex with Obinutuzumab Fab · the same entry in another collection · chain A against A, TM-score 1.00
P11836 · AlphaFold monomer V2.0 prediction for B-lymphocyte antigen CD20 (P11836) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P11836
Elsewhere: RCSB PDB 6Y9A · PDBe 6Y9A · UniProt P11836

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