SMTL ID : 2ygq.1

WIF domain-epidermal growth factor (EGF)-like domains 1-3 of human Wnt inhibitory factor 1 in complex with 1,2- dipalmitoylphosphatidylcholine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.95 Å

Oligo State

homo-trimer

Ligands

3 x GU4- YYJ: 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose(Non-covalent)

GU4-YYJ.1: 4 residues within 4Å: Chain A: H.174, K.180, L.182 Ligands: PCF.7 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:H.174, A:H.174, A:H.174, A:K.180 GU4-YYJ.6: 4 residues within 4Å: Chain B: H.174, K.180, L.182 Ligands: PCF.12 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:H.174, B:H.174, B:H.174, B:K.180 GU4-YYJ.11: 4 residues within 4Å: Chain C: H.174, K.180, L.182 Ligands: PCF.2 4 PLIP interactions: 4 interactions with chain C Salt bridges: C:H.174, C:H.174, C:H.174, C:K.180

3 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Non-covalent)

PCF.2: 20 residues within 4Å: Chain A: L.7, I.9, L.17, I.18, I.26, M.46, P.47, I.49, P.50, M.56, F.58, F.72, F.107, F.119, V.121, V.123 Chain C: V.194, T.195 Ligands: GU4-YYJ.11, GU4-YYJ.11 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.7, A:L.7, A:I.9, A:L.17, A:I.26, A:I.49, A:I.49, A:F.58, A:F.72, A:F.107, A:F.119, A:V.121, A:V.121, A:V.123 PCF.7: 20 residues within 4Å: Chain A: V.194, T.195 Chain B: L.7, I.9, L.17, I.18, I.26, M.46, P.47, I.49, P.50, M.56, F.58, F.72, F.107, F.119, V.121, V.123 Ligands: GU4-YYJ.1, GU4-YYJ.1 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.7, B:L.7, B:I.9, B:L.17, B:I.26, B:I.49, B:I.49, B:F.58, B:F.72, B:F.107, B:F.119, B:V.121, B:V.121, B:V.123 PCF.12: 20 residues within 4Å: Chain B: V.194, T.195 Chain C: L.7, I.9, L.17, I.18, I.26, M.46, P.47, I.49, P.50, M.56, F.58, F.72, F.107, F.119, V.121, V.123 Ligands: GU4-YYJ.6, GU4-YYJ.6 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.7, C:L.7, C:I.9, C:L.17, C:I.26, C:I.49, C:I.49, C:F.58, C:F.72, C:F.107, C:F.119, C:V.121, C:V.121, C:V.123

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

NAG.3: 4 residues within 4Å: Chain A: S.55, N.57, V.102 Chain B: E.21 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.102 Hydrogen bonds: A:S.55 NAG.4: 3 residues within 4Å: Chain A: G.204, N.214 Chain B: H.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.204, A:N.214 NAG.8: 4 residues within 4Å: Chain B: S.55, N.57, V.102 Chain C: E.21 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.102 Hydrogen bonds: B:S.55, C:E.21 NAG.9: 3 residues within 4Å: Chain B: G.204, N.214 Chain C: H.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.204, B:N.214 NAG.13: 4 residues within 4Å: Chain A: E.21 Chain C: S.55, N.57, V.102 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.102 Hydrogen bonds: C:S.55 NAG.14: 3 residues within 4Å: Chain A: H.37 Chain C: G.204, N.214 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.204, C:N.214

3 x FUC: alpha-L-fucopyranose(Post Translational Modification)

FUC.5: 3 residues within 4Å: Chain A: G.222, T.224, I.232 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.232 FUC.10: 3 residues within 4Å: Chain B: G.222, T.224, I.232 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.232 FUC.15: 3 residues within 4Å: Chain C: G.222, T.224, I.232 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malinauskas, T. et al., Modular Mechanism of Wnt Signaling Inhibition by Wnt Inhibitory Factor 1. Nat.Struct.Mol.Biol. (2011)

Release Date

2011-07-13

Peptides

WNT INHIBITORY FACTOR 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

WNT INHIBITORY FACTOR 1