SMTL ID : 4krp.1

Nanobody/VHH domain 9G8 in complex with the extracellular region of EGFR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 13 residues within 4Å: Chain A: E.320, F.321, D.323, S.324, L.325, S.326, N.328, T.330, N.331, V.350, D.355, T.358, T.360 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.323, A:D.323 NAG-NAG.2: 6 residues within 4Å: Chain A: E.388, N.389, T.391, N.420, T.422, N.444 No protein-ligand interaction detected (PLIP)

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: K.311, K.336, N.337 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.337 NAG.4: 2 residues within 4Å: Chain A: N.389, R.390 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.389, A:N.389 NAG.5: 3 residues within 4Å: Chain A: R.503, N.504, D.513 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.513 NAG.6: 2 residues within 4Å: Chain D: Q.86, N.88 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmitz, K.R. et al., Structural Evaluation of EGFR Inhibition Mechanisms for Nanobodies/VHH Domains. Structure (2013)

Release Date

2013-08-28

Peptides

Epidermal growth factor receptor: A
Nanobody/VHH domain 9G8: B
Cetuximab light chain: C
Cetuximab heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Epidermal growth factor receptor

Nanobody/VHH domain 9G8

Cetuximab light chain

Cetuximab heavy chain

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