MolNFT v1 · #83770 · protein

Structure of HER2 with an Fab

3WSQ · Receptor tyrosine-protein kinase erbb-2: “Structure of HER2 with an Fab”. X-ray diffraction, 9 pockets (best druggability 0.76). MolNFT v1 #83770 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3WSQ
Type: protein
Length: 988 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor tyrosine-protein kinase erbb-2; Antibody light chain; Antibody heavy chain
EC: 2.7.10.1
UniProt: P04626
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1)	protein	555	7% helix, 20% strand	P04626
L	Antibody light chain	protein	215	3% helix, 39% strand	—
H	Antibody heavy chain	protein	218	6% helix, 40% strand	—

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	946	0.76	0.79	106	empty
2	558	0.68	0.78	73	empty
3	585	0.65	0.76	49	empty
4	187	0.58	0.81	29	empty
5	152	0.46	0.76	26	empty

Interfaces

3 interfaces between chains.

L–H · 1897 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 513 Å² buried · 5 hydrogen bonds · protein-protein
A–L · 169 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 25 disulfide (disulfide).

Compared structures

3WSQ · Structure of HER2 with an Fab · the same entry in another collection · chain A against A, 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 A 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 3WSQ · PDBe 3WSQ · UniProt P04626

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