MolNFT v1 · #137325 · protein

CD22 D1-D3 in complex with therapeutic Fab epratuzumab

5VL3 · B-cell receptor CD22: “CD22 D1-D3 in complex with therapeutic Fab epratuzumab”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.65). MolNFT v1 #137325 on GenesisL1: 3D structure, binding sites and…

PDB: 5VL3
Type: protein
Length: 2,883 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-cell receptor CD22; Epratuzumab Fab heavy chain; Epratuzumab Fab light chain
UniProt: P20273, S6B291, Q8TCD0
Ligands: NAG, BMA, MAN
Pockets: 20 · best druggability 0.65

Structure

x-ray diffraction · 9 distinct chains · 5% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Q	B-cell receptor CD22	protein	303	5% helix, 51% strand	P20273
R	B-cell receptor CD22	protein	290	3% helix, 54% strand	P20273
S	B-cell receptor CD22	protein	299	3% helix, 53% strand	P20273
T	B-cell receptor CD22	protein	289	3% helix, 52% strand	P20273
A, H	Epratuzumab Fab heavy chain	protein	214	8% helix, 53% strand	S6B291
C	Epratuzumab Fab heavy chain	protein	212	7% helix, 51% strand	S6B291
E	Epratuzumab Fab heavy chain	protein	207	6% helix, 53% strand	S6B291
B, F, L	Epratuzumab Fab light chain	protein	213	7% helix, 51% strand	Q8TCD0
D	Epratuzumab Fab light chain	protein	216	6% helix, 51% strand	Q8TCD0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains Q, H, R, A, S, C, T, E
BMA · beta-D-mannopyranose · sugar · 4 copies · chains Q, R, S, T
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains Q, R, T
GOL · Glycerol · additive · chains S, C, D

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	244	0.65	0.83	33	empty
2	52	0.63	0.93	15	empty
3	253	0.63	0.82	44	empty
4	421	0.61	0.76	45	empty
5	507	0.61	0.75	54	empty

Interfaces

17 interfaces between chains.

E–F · 1895 Å² buried · 12 hydrogen bonds · protein-protein
H–L · 1854 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1841 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1763 Å² buried · 9 hydrogen bonds · protein-protein
Q–H · 838 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

5VL3 · CD22 d1-d3 in complex with therapeutic Fab Epratuzumab · 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
Every structure of UniProt P20273
Every structure of UniProt S6B291
Every structure of UniProt Q8TCD0
Elsewhere: RCSB PDB 5VL3 · PDBe 5VL3 · UniProt P20273 · UniProt S6B291 · UniProt Q8TCD0

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