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HER2 in complex with Fab MF3958

Analyse HER2 in complex with Fab MF3958 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5O4G
Type: protein
Length: 960 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor tyrosine-protein kinase erbb-2; MF3958 Fab light chain; MF3958 Fab heavy chain
EC: 2.7.10.1
UniProt: P04626
Ligands: NAG, MAN, BMA
Pockets: 11 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1)	protein	530	11% helix, 25% strand	P04626
A	MF3958 Fab light chain	protein	214	3% helix, 47% strand	—
B	MF3958 Fab heavy chain	protein	216	7% helix, 44% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C
MAN · alpha-D-mannopyranose · sugar · 3 copies
BMA · beta-D-mannopyranose · sugar

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	710	0.66	0.75	64	empty
2	460	0.65	0.77	55	empty
3	178	0.61	0.83	26	empty
4	102	0.48	0.80	23	empty
5	137	0.45	0.77	25	empty

Interfaces

3 interfaces between chains.

A–B · 1791 Å² buried · 10 hydrogen bonds · protein-protein
C–B · 688 Å² buried · 15 hydrogen bonds · protein-protein
C–A · 39 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

5O4G · HER2 in complex with Fab MF3958 · the same entry in another collection · chain C against C, TM-score 1.00
P04626 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-2 (P04626) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P04626
Elsewhere: RCSB PDB 5O4G · PDBe 5O4G · UniProt P04626

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