SMTL ID : 8pe9.1

Complex between DDR1 DS-like domain and PRTH-101 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 7 residues within 4Å: Chain A: N.73, H.74, F.76, F.165, A.166 Chain C: S.27, Y.89 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.27

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: Q.43, D.46, V.48, S.173, E.174 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Q.43, A:D.46, A:V.48, A:S.173, A:E.174

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

NAG.3: 4 residues within 4Å: Chain A: N.24, D.25, S.26, W.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.24, A:S.26

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 1 residues within 4Å: Chain A: D.180 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.180 ZN.6: 3 residues within 4Å: Chain B: D.102 Chain C: D.52, L.53 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.52, B:D.102 ZN.7: 3 residues within 4Å: Chain B: H.172 Chain C: N.136, N.137 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.172

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: F.76, Y.80, E.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.80, A:E.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., A highly selective humanized DDR1 mAb reverses immune exclusion by disrupting collagen fiber alignment in breast cancer. J Immunother Cancer (2023)

Release Date

2023-06-28

Peptides

Epithelial discoidin domain-containing receptor 1: A
PRTH-101 Fab, heavy chain: B
PRTH-101 Fab, light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Epithelial discoidin domain-containing receptor 1

PRTH-101 Fab, heavy chain

PRTH-101 Fab, light chain