SMTL ID : 6o3a.1

Crystal structure of Frizzled 7 CRD in complex with F7.B Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.1: 9 residues within 4Å: Chain A: Y.92, S.93 Chain B: W.104 Chain C: Q.44, F.45, M.94, F.99, Q.100, P.102 7 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:Y.92, C:F.45, C:F.99, C:F.99, C:P.102, B:W.104 Hydrogen bonds: C:Q.44

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: Q.38, K.39, P.40, G.41, K.42 Chain B: Q.39, Y.95 Ligands: EDO.5 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.41, A:K.42, B:Y.95, B:Y.95 EDO.3: 8 residues within 4Å: Chain A: Q.37, K.39, K.45, P.59, R.61, F.62, E.81, D.82 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.37, A:K.39, A:K.45, A:K.45, A:D.82, A:D.82 EDO.4: 7 residues within 4Å: Chain A: S.31, S.50, S.52, S.53 Chain C: N.95, K.96, G.98 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.31, A:S.31, A:S.53 Water bridges: A:S.50, A:S.50, C:G.98, C:G.98 EDO.5: 7 residues within 4Å: Chain A: Q.38, K.39, P.40, A.84, T.85, K.102 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.85 EDO.8: 6 residues within 4Å: Chain A: T.177 Chain B: L.148, V.176, S.184, L.185, S.186 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.186 Water bridges: B:S.186, B:S.186, A:T.177, A:T.177 EDO.9: 6 residues within 4Å: Chain B: P.41, T.91, L.115, T.117, E.155, Y.183 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.117

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

NA.6: 2 residues within 4Å: Chain A: S.77, Q.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.77, A:S.77, A:Q.79

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

NAG.7: 5 residues within 4Å: Chain B: N.28, S.30, S.31, Y.55 Chain C: K.50 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.28, B:Y.55, B:Y.55, C:K.50 NAG.10: 1 residues within 4Å: Chain C: N.22 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raman, S. et al., Structure-guided design fine-tunes pharmacokinetics, tolerability, and antitumor profile of multispecific frizzled antibodies. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2019-04-03

Peptides

Antibody F7.B Fab, Light chain: A
Antibody F7.B Fab, Heavy chain: B
Frizzled-7: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

Antibody F7.B Fab, Light chain

Antibody F7.B Fab, Heavy chain

Frizzled-7