MolNFT v1 · #128911 · protein

HER3 in complex with Fab MF3178

5O4O · MF3178 Fab light chain: “HER3 in complex with Fab MF3178”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.52). MolNFT v1 #128911 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5O4O
Type: protein
Length: 776 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MF3178 Fab light chain; MF3178 Fab heavy chain; Receptor tyrosine-protein kinase erbb-3
EC: 2.7.10.1
UniProt: P21860
Ligands: NAG
Pockets: 7 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MF3178 Fab light chain	protein	213	5% helix, 50% strand	—
B	MF3178 Fab heavy chain	protein	216	7% helix, 52% strand	—
C	Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1)	protein	347	10% helix, 29% strand	P21860

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C

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

Pockets

7 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	323	0.52	0.74	46	empty
2	283	0.52	0.74	35	empty
3	61	0.47	0.85	20	empty
4	77	0.34	0.75	12	empty
5	63	0.27	0.72	17	empty

Interfaces

3 interfaces between chains.

A–B · 1717 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 263 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 248 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

5O4O · HER3 in complex with Fab MF3178 · the same entry in another collection · chain A against A, 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 C 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 P21860
Elsewhere: RCSB PDB 5O4O · PDBe 5O4O · UniProt P21860

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