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Antibodies specifically targeting a locally misfolded region of tumor associated EGFR

Analyse Antibodies specifically targeting a locally misfolded region of tumor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3G5X
Type: protein
Length: 860 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 806 light chain; 806 heavy chain
Pockets: 11 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	806 light chain	protein	214	5% helix, 51% strand	—
B, D	806 heavy chain	protein	216	4% helix, 51% strand	—

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	489	0.63	0.76	50	empty
2	309	0.52	0.74	39	empty
3	270	0.51	0.74	41	empty
4	174	0.45	0.75	29	empty
5	132	0.44	0.76	23	empty

Interfaces

3 interfaces between chains.

C–D · 2096 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2081 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 640 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

3G5X · Antibodies Specifically Targeting a Locally Misfolded Region of Tumor Associated EGFR · the same entry in another collection · chain D against D, 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
Elsewhere: RCSB PDB 3G5X · PDBe 3G5X

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