SMTL ID : 6bd4.1

Crystal structure of human apo-Frizzled4 receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.282, C.285, C.315, C.318 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.282, A:C.285, A:C.315, A:C.318

4 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 9 residues within 4Å: Chain A: F.343, L.346, Y.347, P.350, M.386, L.389, V.390, T.393, W.397 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.397 OLC.3: 11 residues within 4Å: Chain A: S.69, S.71, F.75, W.79, W.83, D.374, M.377, A.378, M.381, L.382, F.385 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.75, A:W.79, A:W.83, A:M.381, A:L.382, A:L.382, A:F.385, A:F.385, A:F.385 Hydrogen bonds: A:S.69, A:S.71, A:D.374 OLC.4: 7 residues within 4Å: Chain A: Y.107, R.110, F.114, F.168, S.201, H.205, W.209 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.168, A:W.209 Hydrogen bonds: A:R.110, A:S.201, A:S.201 Salt bridges: A:H.205 OLC.5: 5 residues within 4Å: Chain A: V.132, N.156, T.157, G.158, I.161 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.132, A:V.132, A:I.161 Hydrogen bonds: A:N.156, A:T.157, A:G.158

5 x OLA: OLEIC ACID(Non-covalent)(Non-functional Binders)

OLA.6: 11 residues within 4Å: Chain A: I.175, V.178, L.182, H.200, F.204, A.207, I.211, P.251, T.254, Y.255, I.258 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.175, A:I.175, A:V.178, A:L.182, A:F.204, A:F.204, A:A.207, A:I.211, A:T.254, A:I.258 OLA.7: 4 residues within 4Å: Chain A: H.200, Y.203, I.206, A.207 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.203, A:Y.203, A:I.206, A:A.207 Salt bridges: A:H.200 OLA.8: 7 residues within 4Å: Chain A: T.245, V.249, A.250, F.253, L.256, T.352, I.355 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.245, A:V.249, A:F.253, A:F.253, A:F.253, A:F.253, A:L.256, A:T.352, A:I.355 OLA.9: 1 residues within 4Å: Ligands: SO4.13 No protein-ligand interaction detected (PLIP) OLA.10: 4 residues within 4Å: Chain A: V.214, I.217, V.218, I.221 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.214, A:V.214, A:I.217, A:I.217, A:V.218, A:I.221

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 1 residues within 4Å: Chain A: F.271 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.274 SO4.12: 5 residues within 4Å: Chain A: Q.239, N.240, L.241, W.365, R.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.240, A:L.241 Salt bridges: A:R.369 SO4.13: 3 residues within 4Å: Chain A: S.202, Y.203 Ligands: OLA.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.202

4 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.14: 2 residues within 4Å: Ligands: UNX.15, UNX.17 No protein-ligand interaction detected (PLIP) UNX.15: 5 residues within 4Å: Chain A: Y.119, S.387 Ligands: UNX.14, UNX.16, UNX.17 No protein-ligand interaction detected (PLIP) UNX.16: 4 residues within 4Å: Chain A: Y.119, M.386 Ligands: UNX.15, UNX.17 No protein-ligand interaction detected (PLIP) UNX.17: 4 residues within 4Å: Chain A: L.252 Ligands: UNX.14, UNX.15, UNX.16 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, S. et al., Crystal structure of the Frizzled 4 receptor in a ligand-free state. Nature (2018)

Release Date

2018-08-22

Peptides

Frizzled-4/Rubredoxin chimeric protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Frizzled-4/Rubredoxin chimeric protein