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Dual specific BH1 Fab in complex with the extracellular domain of HER2/ERBB-2

Analyse Dual specific BH1 Fab in complex with the extracellular domain of HER2/ERBB-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BE1
Type: protein
Length: 1,012 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor tyrosine-protein kinase erbb-2; Fab fragment-heavy chain; Fab fragment-light…
EC: 2.7.10.1
UniProt: P04626
Ligands: NAG
Pockets: 10 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1)	protein	583	11% helix, 26% strand	P04626
H	Fab fragment-heavy chain	protein	213	4% helix, 46% strand	—
L	Fab fragment-light chain	protein	216	5% helix, 48% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains H, L

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

Pockets

10 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	716	0.70	0.77	97	empty
2	573	0.63	0.75	59	empty
3	125	0.43	0.76	20	empty
4	95	0.39	0.76	19	empty
5	91	0.35	0.75	23	empty

Interfaces

3 interfaces between chains.

H–L · 1772 Å² buried · 10 hydrogen bonds · protein-protein
A–L · 452 Å² buried · 9 hydrogen bonds · protein-protein
A–H · 431 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 26 disulfide (disulfide).

Compared structures

3BE1 · Dual specific bH1 Fab in complex with the extracellular domain of HER2/ErbB-2 · 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 0.94

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 3BE1 · PDBe 3BE1 · UniProt P04626

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