MolNFT v1 · #74582 · protein

Anti-EGFR/HER3 Fab DL11 in complex with domains I-III of the HER3 extracellular region

3P11 · Fab DL11 heavy chain: “Anti-EGFR/HER3 Fab DL11 in complex with domains I-III of the HER3 extracellular region”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.62). MolNFT v1 #74582 on GenesisL1: 3D structure…

PDB: 3P11
Type: protein
Length: 935 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab DL11 heavy chain; Fab DL11 light chain; Receptor tyrosine-protein kinase erbb-3
EC: 2.7.10.1
UniProt: P21860
Ligands: NAG
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab DL11 heavy chain	protein	218	4% helix, 53% strand	—
L	Fab DL11 light chain	protein	211	6% helix, 52% strand	—
A	Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1)	protein	506	10% helix, 26% strand	P21860

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A

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	240	0.62	0.81	33	empty
2	567	0.61	0.74	56	empty
3	137	0.47	0.78	32	empty
4	55	0.40	0.81	20	empty
5	62	0.38	0.79	13	empty

Interfaces

3 interfaces between chains.

H–L · 1877 Å² buried · 15 hydrogen bonds · protein-protein
H–A · 729 Å² buried · 14 hydrogen bonds · protein-protein
L–A · 258 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

3P11 · anti-EGFR/HER3 Fab DL11 in complex with domains I-III of the HER3 extracellular region · 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 0.87

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 3P11 · PDBe 3P11 · UniProt P21860

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