MolNFT v1 · #121547 · protein

Structure of IgE complexed with omalizumab

5HYS · Epididymis luminal protein 214: “Structure of IgE complexed with omalizumab”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.70). MolNFT v1 #121547 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5HYS
Type: protein
Length: 2,604 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epididymis luminal protein 214; Uncharacterized protein; Ig epsilon chain C region
UniProt: P01854
Ligands: NAG, MAN, BMA, SO4
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 6 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A, C	Epididymis luminal protein 214	protein	222	9% helix, 55% strand	—
L, B, D	Uncharacterized protein	protein	217	6% helix, 53% strand	—
E	Epididymis luminal protein 214	protein	218	6% helix, 55% strand	—
F	Uncharacterized protein	protein	215	7% helix, 53% strand	—
G, J	Ig epsilon chain C region	protein	214	9% helix, 47% strand	P01854
I, K	Ig epsilon chain C region	protein	213	9% helix, 48% strand	P01854

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains G, I, J, K
MAN · alpha-D-mannopyranose · sugar · 8 copies · chains G, I, J, K
BMA · beta-D-mannopyranose · sugar · 4 copies · chains G, I, J, K
SO4 · Sulfate ion · ion · 48 copies · chains H, L, B, A, J, G, C, D, F, E, I, K

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	666	0.70	0.78	69	SO4
2	719	0.69	0.77	79	empty
3	681	0.69	0.77	89	SO4
4	615	0.63	0.75	61	SO4
5	543	0.61	0.74	45	SO4

Interfaces

24 interfaces between chains.

C–D · 2056 Å² buried · 19 hydrogen bonds · protein-protein
H–L · 2003 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1871 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1831 Å² buried · 15 hydrogen bonds · protein-protein
J–K · 1548 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 26 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

5HYS · Structure of IgE complexed with omalizumab · the same entry in another collection · chain K against K, 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 P01854
Elsewhere: RCSB PDB 5HYS · PDBe 5HYS · UniProt P01854

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