SMTL ID : 8q7o.1

Crystal structure of the FZD3 cysteine-rich domain in complex with a nanobody (14478)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-2-2-mer

Ligands

2 x DMS: DIMETHYL SULFOXIDE

DMS.1: 3 residues within 4Å: Chain A: E.108, Y.109, D.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.110 pi-Cation interactions: A:Y.111 DMS.7: 5 residues within 4Å: Chain A: Y.106 Chain C: V.47, D.50, R.53, R.56 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.56 Salt bridges: C:D.50

3 x GOL: GLYCEROL

GOL.2: 4 residues within 4Å: Chain B: R.41, A.63, D.64, S.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.41, B:D.64, B:S.65, B:S.65 GOL.6: 7 residues within 4Å: Chain C: T.22, F.23, M.24, P.25, D.32, Y.63, P.65 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Water bridges: C:F.23, C:D.32, C:D.32, C:Y.63, D:D.32 GOL.8: 8 residues within 4Å: Chain C: Y.31 Chain D: A.39, P.42, F.43, Y.63, V.97, P.98, P.100 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.63, D:Y.63, D:P.98, C:Y.31, C:Y.31

1 x CIT: CITRIC ACID

CIT.3: 6 residues within 4Å: Chain B: Y.40, R.48, N.99, D.110, W.112 Chain D: K.90 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Water bridges: D:E.93, B:Y.40 Salt bridges: D:K.90, D:K.90, B:R.48 Hydrogen bonds: B:R.48, B:N.99

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.4: 1 residues within 4Å: Chain C: N.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.20 NAG.9: 1 residues within 4Å: Chain D: N.20 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.20

3 x SO4: SULFATE ION

SO4.5: 7 residues within 4Å: Chain A: T.55, G.57, G.58, S.59 Chain C: H.44, P.45, N.48 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:N.48, A:T.55, A:T.55, A:S.59, A:S.59 Salt bridges: C:H.44 SO4.10: 4 residues within 4Å: Chain D: Y.85, W.99, E.104, C.105 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:C.105 SO4.11: 3 residues within 4Å: Chain D: R.78, Q.82, D.110 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.82, D:Q.82 Water bridges: D:D.110 Salt bridges: D:R.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hillier, J. et al., Structural insights into Frizzled3 through nanobody modulators. Nat Commun (2024)

Release Date

2024-08-28

Peptides

Nanobody 14478: AB
Frizzled-3: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Nanobody 14478

Frizzled-3