MolNFT v1 · #103073 · protein

HER3 extracellular domain in complex with Fab fragment of MOR09825

4P59 · Receptor tyrosine-protein kinase erbb-3: “HER3 extracellular domain in complex with Fab fragment of MOR09825”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.60). MolNFT v1 #103073 on GenesisL1: 3D structure…

PDB: 4P59
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; MOR09825 Fab fragment heavy chain; MOR09825 Fab…
EC: 2.7.10.1
UniProt: P21860
Ligands: NAG
Pockets: 10 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1)	protein	592	6% helix, 27% strand	P21860
H	MOR09825 Fab fragment heavy chain	protein	210	6% helix, 53% strand	—
L	MOR09825 Fab fragment light chain	protein	211	6% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	67	0.60	0.91	20	empty
2	296	0.57	0.77	26	empty
3	423	0.57	0.74	57	empty
4	53	0.53	0.88	17	empty
5	132	0.52	0.80	25	empty

Interfaces

3 interfaces between chains.

H–L · 1653 Å² buried · 16 hydrogen bonds · protein-protein
A–H · 727 Å² buried · 6 hydrogen bonds · protein-protein
A–L · 618 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 29 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

4P59 · HER3 extracellular domain in complex with Fab fragment of MOR09825 · the same entry in another collection · chain H against H, 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 A against A, TM-score 0.83

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 4P59 · PDBe 4P59 · UniProt P21860

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