Research workbench

HER3 in complex with Fab MF3178

Analyse HER3 in complex with Fab MF3178 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5O7P
Type: protein
Length: 1,013 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor tyrosine-protein kinase erbb-3; MF3178 Fab light chain; MF3178 Fab heavy chain
EC: 2.7.10.1
UniProt: P21860
Ligands: NAG, BMA
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1)	protein	582	8% helix, 28% strand	P21860
A	MF3178 Fab light chain	protein	213	5% helix, 48% strand	—
B	MF3178 Fab heavy chain	protein	218	7% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains C
BMA · beta-D-mannopyranose · sugar · chains C

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

Pockets

9 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	64	0.75	0.98	21	empty
2	496	0.64	0.77	38	empty
3	141	0.47	0.78	24	empty
4	214	0.45	0.73	30	empty
5	104	0.37	0.75	17	empty

Interfaces

3 interfaces between chains.

A–B · 1796 Å² buried · 12 hydrogen bonds · protein-protein
C–B · 276 Å² buried · 1 hydrogen bond · protein-protein
C–A · 208 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

5O7P · HER3 in complex with Fab MF3178 · the same entry in another collection · chain C against C, TM-score 1.00
P21860 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-3 (P21860) · a predicted model of the same protein · chain C against A, TM-score 0.80

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 P21860
Elsewhere: RCSB PDB 5O7P · PDBe 5O7P · UniProt P21860

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