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Structure of full-length CD20 in complex with rituximab Fab

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

PDB: 6Y90
Type: protein
Length: 1,218 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-lymphocyte antigen CD20; Rituximab Fab heavy chain; Rituximab Fab light chain
UniProt: P11836
Ligands: MYS, Y01, PC1
Pockets: 17 · best druggability 0.87

Structure

electron microscopy · 3 distinct chains · 21% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	B-lymphocyte antigen CD20	protein	172	67% helix, 0% strand	P11836
C, H	Rituximab Fab heavy chain	protein	224	0% helix, 46% strand	—
D, L	Rituximab Fab light chain	protein	213	7% helix, 46% strand	—

Ligands and binding sites

MYS · Pentadecane · ligand · 10 copies · chains A, B
Y01 · Cholesterol hemisuccinate · ligand · 8 copies · chains A, B
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	545	0.87	0.93	60	empty
2	119	0.62	0.87	24	empty
3	110	0.61	0.87	20	empty
4	569	0.60	0.74	58	empty
5	543	0.60	0.74	61	empty

Interfaces

14 interfaces between chains.

H–L · 2001 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 2000 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1638 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 494 Å² buried · 6 hydrogen bonds · protein-protein
A–H · 489 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

6Y90 · Structure of full-length CD20 in complex with Rituximab Fab · the same entry in another collection · chain L against L, TM-score 1.00
P11836 · AlphaFold monomer V2.0 prediction for B-lymphocyte antigen CD20 (P11836) · a predicted model of the same protein · chain B 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 P11836
Elsewhere: RCSB PDB 6Y90 · PDBe 6Y90 · UniProt P11836

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