SMTL ID : 8kcw.1

Cryo-EM structure of human SIDT1 bound to cholesterol

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: V.51, Y.81, N.83, E.124, L.162 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 1 residues within 4Å: Chain A: N.136 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain B: V.51, Y.81, N.83, E.124, L.162 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 1 residues within 4Å: Chain B: N.136 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 3 residues within 4Å: Chain A: N.67, Q.142, L.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.142 NAG-NAG.4: 4 residues within 4Å: Chain A: V.55, N.57, S.59, T.60 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.67, Q.142, L.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.142 NAG-NAG.8: 4 residues within 4Å: Chain B: V.55, N.57, S.59, T.60 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.9: 4 residues within 4Å: Chain A: H.563, D.574, H.791, H.795 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.563, A:D.574, A:D.574, A:H.791, A:H.795 ZN.12: 4 residues within 4Å: Chain B: H.563, D.574, H.791, H.795 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.563, B:D.574, B:D.574, B:H.791, B:H.795

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.10: 12 residues within 4Å: Chain A: Y.579, M.580, G.583, L.587, A.599, S.603, A.604, S.607, F.608, V.611, F.717 Ligands: CLR.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.587, A:F.608, A:V.611, A:F.717 CLR.11: 8 residues within 4Å: Chain A: G.583, M.586, L.587, Y.590, I.597, Q.646, I.647 Ligands: CLR.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.587, A:L.587, A:Y.590, A:Y.590, A:Y.590, A:Y.590, A:I.597, A:Q.646 CLR.13: 12 residues within 4Å: Chain B: Y.579, M.580, G.583, L.587, A.599, S.603, A.604, S.607, F.608, V.611, F.717 Ligands: CLR.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.587, B:F.608, B:V.611, B:F.717 CLR.14: 8 residues within 4Å: Chain B: G.583, M.586, L.587, Y.590, I.597, Q.646, I.647 Ligands: CLR.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.587, B:L.587, B:Y.590, B:Y.590, B:Y.590, B:Y.590, B:I.597, B:Q.646

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirano, Y. et al., Cryo-EM analysis reveals human SID-1 transmembrane family member 1 dynamics underlying lipid hydrolytic activity. Commun Biol (2024)

Release Date

2024-06-12

Peptides

SID1 transmembrane family member 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Membrane

We predict this structure to be a membrane protein.
Show / Hide

SID1 transmembrane family member 1

Related Entries With Identical Sequence