SMTL ID : 2ygo.1

WIF domain-EGF-like domain 1 of human Wnt inhibitory factor 1 in complex with 1,2-dipalmitoylphosphatidylcholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

PCF.1: 20 residues within 4Å: Chain A: L.7, I.9, L.17, I.18, I.24, I.26, M.32, F.35, R.45, M.46, P.47, I.49, M.56, F.58, F.119, V.121, V.123, V.125, K.135, F.142 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.7, A:I.9, A:L.17, A:I.26, A:I.49, A:F.58, A:F.119, A:V.121, A:V.123, A:V.125, A:F.142, A:F.142 Salt bridges: A:R.45 PCF.4: 20 residues within 4Å: Chain B: L.7, I.9, L.17, I.18, I.24, I.26, M.32, F.35, R.45, M.46, P.47, I.49, M.56, F.58, F.119, V.121, V.123, V.125, K.135, F.142 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.7, B:I.9, B:L.17, B:I.26, B:I.49, B:F.58, B:F.119, B:V.121, B:V.123, B:V.125, B:F.142, B:F.142 Salt bridges: B:R.45

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

NAG.2: 5 residues within 4Å: Chain A: H.12, Q.13, N.57, V.102, Q.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.12, A:N.57 Water bridges: A:Q.13, A:N.57 NAG.5: 5 residues within 4Å: Chain B: H.12, Q.13, N.57, V.102, Q.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.12, B:N.57 Water bridges: B:Q.13, B:N.57

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

NA.3: 2 residues within 4Å: Chain A: C.155, G.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.155, A:G.159 NA.6: 2 residues within 4Å: Chain B: C.155, G.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.155, B:G.159

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

WNT INHIBITORY FACTOR 1