MolNFT v1 · #143580 · protein

Crystal structure of the Fab fragment of necitumumab (FAB11F8) in complex with domain III from a cetuximab resistant variant of EGFR (SEGFRD3-S468R)

6B3S · Epidermal growth factor receptor: “Crystal structure of the Fab fragment of necitumumab (FAB11F8) in complex with domain III from a cetuximab…”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.80).…

PDB: 6B3S
Type: protein
Length: 2,478 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epidermal growth factor receptor; Necitumumab Fab heavy chain; Necitumumab Fab light chain
EC: 2.7.10.1
UniProt: P00533
Ligands: NAG, BMA, MAN
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 10% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Epidermal growth factor receptor (EC 2.7.10.1)	protein	191	18% helix, 23% strand	P00533
H, C, J	Necitumumab Fab heavy chain	protein	213	5% helix, 53% strand	—
L, D, G, K	Necitumumab Fab light chain	protein	213	6% helix, 50% strand	—
B, E, I	Epidermal growth factor receptor (EC 2.7.10.1)	protein	194	20% helix, 22% strand	P00533
F	Necitumumab Fab heavy chain	protein	214	6% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B, E, I
BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, E
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B, E

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	724	0.80	0.84	104	empty
2	509	0.74	0.83	77	empty
3	367	0.68	0.81	61	empty
4	291	0.58	0.78	40	empty
5	142	0.55	0.82	22	empty

Interfaces

17 interfaces between chains.

F–G · 1590 Å² buried · 14 hydrogen bonds · protein-protein
H–L · 1585 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1569 Å² buried · 14 hydrogen bonds · protein-protein
J–K · 1564 Å² buried · 14 hydrogen bonds · protein-protein
G–K · 1007 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide, 15 glycan (disulfide, N-glycosylation).

Compared structures

6B3S · Crystal structure of the Fab fragment of necitumumab (Fab11F8) in complex with domain III… · the same entry in another collection · chain K against K, TM-score 1.00

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 P00533
Elsewhere: RCSB PDB 6B3S · PDBe 6B3S · UniProt P00533

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