SMTL ID : 8zxd.1

the Planar Cell Polarity Core Protein Vangl1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 7 residues within 4Å: Chain A: V.184, L.188, V.191, L.195, A.470, T.472 Ligands: Y01.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.184, A:L.188, A:V.191, A:L.195, A:A.470, A:T.472 Y01.3: 9 residues within 4Å: Chain A: V.184, L.188, R.244, T.472, G.474 Chain B: L.161, L.164, W.168 Ligands: Y01.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.184, A:L.188, B:L.164, B:W.168 Salt bridges: A:R.244 Y01.4: 7 residues within 4Å: Chain B: V.184, L.188, V.191, L.195, A.470, T.472 Ligands: Y01.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.184, B:V.191, B:L.195, B:A.470, B:T.472 Y01.6: 9 residues within 4Å: Chain B: V.184, L.188, R.244, T.472, G.474 Chain C: L.161, L.164, W.168 Ligands: Y01.4 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.164, C:W.168, B:V.184, B:L.188 Salt bridges: B:R.244 Y01.7: 9 residues within 4Å: Chain A: L.161, L.164, W.168 Chain C: V.184, L.188, R.244, T.472, G.474 Ligands: Y01.8 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.164, A:W.168, C:V.184, C:L.188 Salt bridges: C:R.244 Y01.8: 7 residues within 4Å: Chain C: V.184, L.188, V.191, L.195, A.470, T.472 Ligands: Y01.7 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.184, C:V.191, C:L.195, C:A.470, C:T.472 Y01.10: 7 residues within 4Å: Chain D: V.184, L.188, V.191, L.195, A.470, T.472 Ligands: Y01.12 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.184, D:V.191, D:L.195, D:A.470, D:T.472 Y01.12: 9 residues within 4Å: Chain D: V.184, L.188, R.244, T.472, G.474 Chain E: L.161, L.164, W.168 Ligands: Y01.10 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:V.184, D:L.188, E:L.164, E:W.168 Salt bridges: D:R.244 Y01.13: 7 residues within 4Å: Chain E: V.184, L.188, V.191, L.195, A.470, T.472 Ligands: Y01.15 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:V.184, E:V.191, E:L.195, E:A.470, E:T.472 Y01.15: 9 residues within 4Å: Chain E: V.184, L.188, R.244, T.472, G.474 Chain F: L.161, L.164, W.168 Ligands: Y01.13 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:L.164, F:W.168, E:V.184, E:L.188 Salt bridges: E:R.244 Y01.16: 9 residues within 4Å: Chain D: L.161, L.164, W.168 Chain F: V.184, L.188, R.244, T.472, G.474 Ligands: Y01.17 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:V.184, F:L.188, D:L.164, D:W.168 Salt bridges: F:R.244 Y01.17: 7 residues within 4Å: Chain F: V.184, L.188, V.191, L.195, A.470, T.472 Ligands: Y01.16 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:V.184, F:V.191, F:L.195, F:A.470, F:T.472

6 x MC3: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

MC3.2: 6 residues within 4Å: Chain A: F.171, R.186, I.193, L.241, R.274 Chain C: Q.247 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.171 Salt bridges: A:R.186, A:R.274 MC3.5: 6 residues within 4Å: Chain A: Q.247 Chain B: F.171, R.186, I.193, L.241, R.274 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.171 Hydrogen bonds: B:R.274 Salt bridges: B:R.186 MC3.9: 6 residues within 4Å: Chain B: Q.247 Chain C: F.171, R.186, I.193, L.241, R.274 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.171 Hydrogen bonds: C:R.274 Salt bridges: C:R.186 MC3.11: 6 residues within 4Å: Chain D: F.171, R.186, I.193, L.241, R.274 Chain F: Q.247 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.171 Salt bridges: D:R.186, D:R.274 MC3.14: 6 residues within 4Å: Chain D: Q.247 Chain E: F.171, R.186, I.193, L.241, R.274 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.171 Hydrogen bonds: E:R.274 Salt bridges: E:R.186 MC3.18: 6 residues within 4Å: Chain E: Q.247 Chain F: F.171, R.186, I.193, L.241, R.274 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.171 Hydrogen bonds: F:R.274 Salt bridges: F:R.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, F. et al., the Planar Cell Polarity Core Protein Vangl1. To Be Published

Release Date

2024-11-27

Peptides

Vang-like protein 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Vang-like protein 1