SMTL ID : 4krl.1

Nanobody/VHH domain 7D12 in complex with domain III of the extracellular region of EGFR, pH 6.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

1 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: 12 residues within 4Å: Chain B: E.14, F.15, D.17, S.18, L.19, S.20, N.22, T.24, N.25, D.49, T.52, T.54 No protein-ligand interaction detected (PLIP)

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 5 residues within 4Å: Chain A: S.52, S.57, A.103, W.104, Y.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.104 Water bridges: A:G.106 MES.6: 4 residues within 4Å: Chain B: K.149, E.183, C.196, R.197 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.149 Salt bridges: B:E.183

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

NAG.3: 3 residues within 4Å: Chain B: K.27, K.30, N.31 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.30 Hydrogen bonds: B:N.31, B:N.31 NAG.4: 4 residues within 4Å: Chain A: Y.109 Chain B: W.80, E.82, N.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.109

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 2 residues within 4Å: Chain A: Q.1 Chain B: H.103 Ligand excluded by 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

Nanobody/VHH domain 7D12: A
Epidermal growth factor receptor: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Nanobody/VHH domain 7D12

Epidermal growth factor receptor

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