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Structure of cetuximab with aminoheptanoic acid-linked N-butylarginine meditope variant

Analyse Structure of cetuximab with aminoheptanoic acid-linked N-butylarginine meditope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AU5
Type: protein
Length: 885 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cetuximab Fab light chain; Cetuximab Fab heavy chain; Meditope
UniProt: P01834, S6B291
Ligands: SO4
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cetuximab Fab light chain	protein	212	6% helix, 50% strand	P01834
B, D	Cetuximab Fab heavy chain	protein	220	7% helix, 51% strand	S6B291
C	Cetuximab Fab light chain	protein	213	6% helix, 51% strand	P01834
E, F	Meditope	protein	10	0% helix, 40% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains B, C, D

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

Pockets

8 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	676	0.72	0.79	84	empty
2	343	0.60	0.77	50	empty
3	322	0.60	0.78	42	empty
4	143	0.45	0.76	23	empty
5	118	0.41	0.76	25	empty

Interfaces

7 interfaces between chains.

C–D · 1868 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1852 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 685 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 495 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 488 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).

Compared structures

6AU5 · Structure of cetuximab with aminoheptanoic acid-linked n-butylarginine meditope variant · the same entry in another collection · chain F against F, TM-score 1.00
P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain C against A, TM-score 0.50

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 P01834
Every structure of UniProt S6B291
Elsewhere: RCSB PDB 6AU5 · PDBe 6AU5 · UniProt P01834 · UniProt S6B291

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