SMTL ID : 7om4.1

Nanobody EgB4 bound to the full extracellular EGFR-EGF complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 6.05 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: Q.28, N.32, N.33, F.54 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.54 Hydrogen bonds: A:Q.28, A:N.33 NAG.2: 1 residues within 4Å: Chain A: N.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.49 NAG.3: 5 residues within 4Å: Chain A: N.91, S.92, D.147, F.148, N.151 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.148 NAG.4: 10 residues within 4Å: Chain A: F.321, S.324, L.325, S.326, N.328, T.330, N.331, D.355, T.358, T.360 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.324, A:L.325, A:S.326, A:N.328, A:N.331, A:N.331, A:T.358, A:T.358 NAG.5: 1 residues within 4Å: Chain A: N.337 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: E.388, T.391, N.420 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.420 NAG.7: 3 residues within 4Å: Chain A: L.485, N.504, D.513 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.485 NAG.8: 4 residues within 4Å: Chain D: Q.28, N.32, N.33, F.54 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.54 Hydrogen bonds: D:Q.28, D:N.33 NAG.9: 1 residues within 4Å: Chain D: N.49 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.49 NAG.10: 5 residues within 4Å: Chain D: N.91, S.92, D.147, F.148, N.151 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.148 NAG.11: 10 residues within 4Å: Chain D: F.321, S.324, L.325, S.326, N.328, T.330, N.331, D.355, T.358, T.360 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.324, D:L.325, D:S.326, D:N.328, D:N.331, D:N.331, D:T.358 NAG.12: 1 residues within 4Å: Chain D: N.337 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain D: E.388, T.391, N.420 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.420 NAG.14: 3 residues within 4Å: Chain D: L.485, N.504, D.513 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeronian, M.R. et al., Structural insights into the non-inhibitory mechanism of the anti-EGFR EgB4 nanobody. Bmc Mol Cell Biol (2022)

Release Date

2022-03-02

Peptides

Epidermal growth factor receptor: AD
Epidermal growth factor: BE
Nanobody EgB4: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
C

E
C

C
B

F
B

Epidermal growth factor receptor

Epidermal growth factor

Nanobody EgB4

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