SMTL ID : 4uzq.1

STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH O-PALMITOLEOYL SERINE - CRYSTAL FORM IX - 1.5A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x SER: PROTEIN WNT-7A(Non-covalent)

SER.1: 7 residues within 4Å: Chain A: G.49, G.50, W.51, A.155, H.312, E.313 Ligands: PAM.8 Protein-ligand interaction information (PLIP) not available SER.9: 7 residues within 4Å: Chain B: G.49, G.50, W.51, A.155, H.312, E.313 Ligands: PAM.16 Protein-ligand interaction information (PLIP) not available

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

NAG.2: 6 residues within 4Å: Chain A: N.19, V.22, L.129, Q.132, E.133, R.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.19, A:E.133, A:R.136 Water bridges: A:Q.132 NAG.10: 6 residues within 4Å: Chain B: N.19, V.22, L.129, Q.132, E.133, R.136 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.19, B:R.136 Water bridges: B:Q.132

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

NA.3: 3 residues within 4Å: Chain A: I.206, T.268, N.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.268, A:N.271 NA.4: 1 residues within 4Å: Chain A: S.362 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.362, A:S.362 NA.11: 3 residues within 4Å: Chain B: I.206, T.268, N.271 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.206, B:N.271 NA.12: 1 residues within 4Å: Chain B: S.362 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.362

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: R.56, N.121, E.122, Y.123, Y.220 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: G.39, N.97 Chain B: Y.94, R.332, H.335 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: V.224, V.225, R.230 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: R.56, N.121, E.122, Y.123, Y.220 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: Y.94, R.332, H.335 Chain B: G.39, N.97 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: V.224, V.225, R.230 Ligand excluded by PLIP

2 x PAM: PALMITOLEIC ACID(Non-covalent)

PAM.8: 17 residues within 4Å: Chain A: G.49, G.50, W.51, Y.52, V.110, A.155, A.156, T.159, F.191, P.210, I.214, F.242, F.243, A.265, V.269, H.312 Ligands: SER.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.51, A:W.51, A:V.110, A:A.156, A:F.191, A:F.191, A:F.191, A:F.191, A:F.191, A:P.210, A:I.214, A:F.242, A:F.243, A:F.243, A:A.265, A:V.269 Hydrogen bonds: A:G.50, A:W.51, A:A.156 PAM.16: 17 residues within 4Å: Chain B: G.49, G.50, W.51, Y.52, V.110, A.155, A.156, T.159, F.191, P.210, I.214, F.242, F.243, A.265, V.269, H.312 Ligands: SER.9 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.51, B:W.51, B:V.110, B:A.156, B:F.191, B:F.191, B:F.191, B:F.191, B:F.191, B:P.210, B:I.214, B:F.242, B:F.243, B:F.243, B:A.265, B:V.269 Hydrogen bonds: B:G.50, B:W.51, B:A.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kakugawa, S. et al., Notum Deacylates Wnt Proteins to Suppress Signalling Activity. Nature (2015)

Release Date

2015-02-25

Peptides

PROTEIN NOTUM HOMOLOG: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PROTEIN NOTUM HOMOLOG

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