MolNFT v1 · #127493 · protein

Crystal structure of a HER2-nb complex

5MY6 · Receptor tyrosine-protein kinase erbb-2: “Crystal structure of a HER2-nb complex”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.65). MolNFT v1 #127493 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5MY6
Type: protein
Length: 671 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor tyrosine-protein kinase erbb-2; Nanobody 2RS15D
EC: 2.7.10.1
UniProt: P04626
Ligands: NAG
Pockets: 8 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1)	protein	556	12% helix, 25% strand	P04626
B	Nanobody 2RS15D	protein	115	3% helix, 56% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

8 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	511	0.65	0.77	53	empty
2	67	0.54	0.87	15	empty
3	103	0.49	0.81	22	empty
4	105	0.49	0.80	20	empty
5	116	0.44	0.78	27	empty

Interfaces

1 interface between chains.

A–B · 783 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5MY6 · Crystal structure of a HER2-Nb complex · 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 0.97

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 5MY6 · PDBe 5MY6 · UniProt P04626

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