SMTL ID : 2ygp.1

WIF domain-EGF-like domain 1 Met77Trp of human Wnt inhibitory factor 1 in complex with 1,2-dipalmitoylphosphatidylcholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-dimer

Ligands

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

PCF.1: 23 residues within 4Å: Chain A: L.7, I.9, L.17, I.18, I.24, I.26, F.35, R.45, W.46, P.47, I.49, M.56, F.58, W.60, F.107, F.119, V.121, V.123, V.125, K.135, T.136, P.137, F.142 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.7, A:L.7, A:I.9, A:I.26, A:W.46, A:I.49, A:I.49, A:F.58, A:W.60, A:F.107, A:F.119, A:V.121, A:V.121, A:V.125, A:F.142, A:F.142, A:F.142, A:F.142 Water bridges: A:R.45 Salt bridges: A:R.45 pi-Cation interactions: A:F.35 PCF.5: 23 residues within 4Å: Chain B: L.7, I.9, L.17, I.18, I.24, I.26, F.35, R.45, W.46, P.47, I.49, M.56, F.58, W.60, F.107, F.119, V.121, V.123, V.125, K.135, T.136, P.137, F.142 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.7, B:L.7, B:I.9, B:I.26, B:W.46, B:I.49, B:I.49, B:F.58, B:W.60, B:F.107, B:F.119, B:V.121, B:V.121, B:V.125, B:F.142, B:F.142, B:F.142, B:F.142 Water bridges: B:R.45 Salt bridges: B:R.45 pi-Cation interactions: B:F.35

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

NAG.2: 6 residues within 4Å: Chain A: H.12, Q.13, V.16, N.57, V.102, Q.104 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.16 Hydrogen bonds: A:H.12, A:N.57 Water bridges: A:Q.13, A:N.57 NAG.6: 6 residues within 4Å: Chain B: H.12, Q.13, V.16, N.57, V.102, Q.104 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.16 Hydrogen bonds: B:H.12, B:N.57 Water bridges: B:Q.13, B:N.57

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: C.151, G.154, C.155, C.161 No protein-ligand interaction detected (PLIP) CA.7: 4 residues within 4Å: Chain B: C.151, G.154, C.155, C.161 No protein-ligand interaction detected (PLIP)

2 x SPD: SPERMIDINE(Non-covalent)

SPD.4: 8 residues within 4Å: Chain A: M.32, T.36, H.37, F.39, K.135, T.136, P.137, Q.138 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.39, A:P.137, A:P.137 Hydrogen bonds: A:Q.138 SPD.8: 8 residues within 4Å: Chain B: M.32, T.36, H.37, F.39, K.135, T.136, P.137, Q.138 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.39, B:P.137, B:P.137 Hydrogen bonds: B:Q.138

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