SMTL ID : 6o39.1

Crystal structure of Frizzled 5 CRD in complex with F2.I Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: G.91, V.92, Y.93, L.94 Chain C: Y.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.92, A:Y.93, A:L.94 EDO.2: 6 residues within 4Å: Chain A: T.177 Chain B: L.148, V.176, S.184, L.185, S.186 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.186 Water bridges: B:S.186, B:S.186, A:S.175, A:T.177, A:T.177 EDO.3: 3 residues within 4Å: Chain A: Y.55 Chain B: D.108, Y.109 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.108, A:Y.55 EDO.4: 5 residues within 4Å: Chain A: V.15, P.80, K.168, D.169, S.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.170 EDO.5: 7 residues within 4Å: Chain A: Q.38, K.39, P.40, G.41, K.42 Chain B: Q.39, Y.95 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.95, A:G.41, A:K.42, A:K.42 EDO.6: 4 residues within 4Å: Chain A: A.143, K.144, V.145, E.160 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.143, A:V.145 Water bridges: A:S.158 EDO.8: 4 residues within 4Å: Chain B: N.162, A.165, L.166, Q.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.162 EDO.9: 6 residues within 4Å: Chain B: L.196, G.197, Q.199, T.200, K.217, E.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.200, B:K.217 EDO.10: 4 residues within 4Å: Chain B: P.41, T.91, E.155, Y.183 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.117, B:E.155 EDO.11: 3 residues within 4Å: Chain A: T.163, D.166 Chain B: H.171 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.166, A:D.166, B:V.170, B:H.171 Water bridges: A:S.167, A:S.173, B:T.172 EDO.12: 6 residues within 4Å: Chain A: D.166 Chain B: T.167, S.168, G.169, V.170, H.171 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.168, B:G.169, B:H.171 EDO.13: 5 residues within 4Å: Chain A: K.42, A.43 Chain B: W.110, G.111, Q.112 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.110, A:A.43 Water bridges: B:W.110, B:Q.112, B:Q.112, A:G.41 EDO.15: 6 residues within 4Å: Chain B: F.27, N.28, S.31 Chain C: D.34, E.35, L.38 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.28, B:N.28, C:D.34

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: Q.37, K.39, K.45, L.47, P.59, F.62 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.59, A:F.62 Water bridges: A:Q.37, A:K.45, A:K.45, A:K.45 Salt bridges: A:K.39, A:K.45

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

NAG.14: 2 residues within 4Å: Chain C: R.15, N.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.15

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 F2.I Fab, Light chain: A
Antibody F2.I Fab, Heavy chain: B
Frizzled-5: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Antibody F2.I Fab, Light chain

Antibody F2.I Fab, Heavy chain

Frizzled-5