SMTL ID : 5xwd.1

Crystal structure of the complex of 059-152-Fv and EGFR-ECD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-MAN-NAG.1: 16 residues within 4Å: Chain A: D.347, S.348, L.349, S.350, N.352, T.354, N.355, D.379, T.382, T.384 Chain B: S.63, V.80, D.81, T.82, S.83 Ligands: ZN.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.347

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

NAG.2: 3 residues within 4Å: Chain A: Q.52, N.56, N.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.52 NAG.3: 4 residues within 4Å: Chain A: S.116, D.171, F.172, N.175 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.172 Hydrogen bonds: A:S.116 NAG.4: 3 residues within 4Å: Chain A: P.195, N.196, I.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.196 NAG.5: 1 residues within 4Å: Chain A: N.361 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.361 NAG.6: 2 residues within 4Å: Chain A: N.444 Chain C: K.37 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.37, A:N.444 NAG.7: 6 residues within 4Å: Chain A: N.528, D.537, K.538, C.539, L.541, V.550 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.539, A:C.539 NAG.8: 1 residues within 4Å: Chain A: N.568 No protein-ligand interaction detected (PLIP)

20 x ZN: ZINC ION(Non-covalent)

ZN.9: 1 residues within 4Å: Chain A: E.45 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.45, A:E.45 ZN.10: 3 residues within 4Å: Chain A: L.144, H.145, D.171 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.145 ZN.11: 5 residues within 4Å: Chain A: T.274, Q.276, D.577, H.590 Ligands: ZN.22 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.590 ZN.12: 6 residues within 4Å: Chain A: T.302, D.303, H.304, K.328 Ligands: ZN.21, ZN.23 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.303 ZN.13: 2 residues within 4Å: Chain A: H.358 Ligands: ZN.19 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.358 ZN.14: 4 residues within 4Å: Chain A: D.393, R.414, H.418, A.419 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.393, A:H.418 ZN.15: 2 residues within 4Å: Chain A: H.584 Ligands: ZN.20 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.584 ZN.16: 3 residues within 4Å: Chain A: D.416, H.418, R.451 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.416, A:D.416 ZN.17: 1 residues within 4Å: Chain A: D.537 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.537 ZN.18: 2 residues within 4Å: Chain A: H.618, L.619 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.618 ZN.19: 3 residues within 4Å: Chain A: E.344, H.358 Ligands: ZN.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.344, A:H.358 ZN.20: 2 residues within 4Å: Chain A: H.584 Ligands: ZN.15 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.584 ZN.21: 4 residues within 4Å: Chain A: D.303, H.304 Ligands: ZN.12, ZN.23 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.303 ZN.22: 4 residues within 4Å: Chain A: Q.276, D.577, H.590 Ligands: ZN.11 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.577, A:H.590 ZN.23: 4 residues within 4Å: Chain A: D.303, H.304 Ligands: ZN.12, ZN.21 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.303, A:H.304 ZN.24: 3 residues within 4Å: Chain B: D.81, S.83 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.83 ZN.25: 4 residues within 4Å: Chain A: H.433 Chain B: R.106, D.115 Ligands: ZN.26 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.433, B:D.115 ZN.26: 3 residues within 4Å: Chain A: H.433 Chain B: D.115 Ligands: ZN.25 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.433, B:D.115, B:D.115 ZN.27: 4 residues within 4Å: Chain B: P.70 Chain C: S.8, S.101, H.103 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.8, C:H.103 ZN.28: 1 residues within 4Å: Chain C: H.103 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsuda, T. et al., Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction. PLoS ONE (2018)

Release Date

2018-02-28

Peptides

Epidermal growth factor receptor: A
VH chain of 059-152: B
VL chain of 059-152: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
D

Epidermal growth factor receptor

VH chain of 059-152

VL chain of 059-152