SMTL ID : 7e2h.1

Cryo-EM structure of hDisp1NNN-3C-Cleavage

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 5 residues within 4Å: Chain B: S.750, L.753, C.841, I.842 Ligands: Y01.2 No protein-ligand interaction detected (PLIP) Y01.2: 7 residues within 4Å: Chain B: L.754, M.822, T.830, T.834, L.838, C.841 Ligands: Y01.1 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.754, B:L.838 Hydrogen bonds: B:W.756 Y01.3: 12 residues within 4Å: Chain B: K.465, M.466, L.468, Y.661, E.662, S.705, L.709, M.712, V.748, L.758, I.766 Ligands: Y01.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:K.465, B:L.468, B:E.662, B:L.709, B:L.709, B:V.748, B:L.758, B:I.766 Hydrogen bonds: B:E.662, B:E.662 Y01.4: 6 residues within 4Å: Chain B: Q.221, L.225, T.228, L.284, L.287, Y.829 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.228, B:L.284, B:L.287 Y01.5: 5 residues within 4Å: Chain A: L.193 Chain B: F.250, M.254, L.382, R.385 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.193, B:F.250, B:F.250, B:L.382 Y01.6: 6 residues within 4Å: Chain B: F.274, F.276, Y.344, Y.347, V.359, N.527 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.274, B:F.276, B:Y.344, B:Y.347, B:V.359 Y01.7: 5 residues within 4Å: Chain B: C.461, K.465, F.745 Ligands: Y01.3, Y01.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.745 Salt bridges: B:K.465 Y01.8: 3 residues within 4Å: Chain B: C.461, I.462 Ligands: Y01.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.462

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

NAG.9: 1 residues within 4Å: Chain B: N.560 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.560 NAG.10: 1 residues within 4Å: Chain B: N.200 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.200 NAG.11: 2 residues within 4Å: Chain B: K.12, N.87 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.87 NAG.12: 1 residues within 4Å: Chain B: N.641 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.641

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Structural insights into proteolytic activation of the human Dispatched1 transporter for Hedgehog morphogen release. Nat Commun (2021)

Release Date

2021-12-08

Peptides

Protein dispatched homolog 1: A
Protein dispatched homolog 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

Membrane

We predict this structure to be a membrane protein.
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Protein dispatched homolog 1

Protein dispatched homolog 1