SMTL ID : 8wos.1

Cryo-EM structure of human SIDT1 protein with C1 symmetry at low pH

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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.1: 3 residues within 4Å: Chain A: N.83, E.124, K.160 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.57, T.60, P.154, L.155 Chain B: R.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.57 NAG-NAG.3: 3 residues within 4Å: Chain B: N.83, E.124, K.160 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: R.36 Chain B: N.57, S.59, T.60, P.154, L.155 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.57, B:S.59

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

NAG.5: 4 residues within 4Å: Chain A: N.67, Y.68, T.69, Q.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.67, A:T.69 NAG.6: 3 residues within 4Å: Chain A: D.73, T.135, N.136 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain B: N.67, Y.68, T.69, Q.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.67, B:T.69 NAG.13: 4 residues within 4Å: Chain B: D.73, T.135, N.136, E.137 No protein-ligand interaction detected (PLIP)

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 3 residues within 4Å: Chain A: A.760, Y.764 Ligands: CLR.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.760, A:Y.764 CLR.8: 10 residues within 4Å: Chain A: S.716, Y.717, G.720, C.724, L.727, L.728, L.763, F.766, F.767 Ligands: CLR.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.727, A:L.727, A:L.728, A:L.763, A:F.766, A:F.767 CLR.9: 4 residues within 4Å: Chain A: I.460, I.464, V.491 Ligands: CLR.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.460, A:I.464, A:V.491 CLR.10: 3 residues within 4Å: Chain A: I.498, L.502 Ligands: CLR.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.498, A:L.502 CLR.14: 7 residues within 4Å: Chain B: L.489, F.495, I.498, N.501, L.502, A.560 Ligands: CLR.17 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.489, B:F.495, B:N.501, B:L.502, B:A.560 CLR.15: 4 residues within 4Å: Chain B: A.756, A.760, Y.764 Ligands: CLR.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.764, B:Y.764, B:Y.764 CLR.16: 9 residues within 4Å: Chain B: S.716, Y.717, G.720, C.724, L.727, L.763, F.766, F.767 Ligands: CLR.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.727, B:L.763, B:F.766 CLR.17: 6 residues within 4Å: Chain B: I.464, T.468, V.491, V.557, C.561 Ligands: CLR.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.464, B:V.491, B:V.557 Hydrogen bonds: B:T.468

2 x ZN: ZINC ION(Non-covalent)

ZN.11: 5 residues within 4Å: Chain A: S.559, H.563, H.796, W.799, H.800 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.563, A:H.796, A:H.800, A:H.800 ZN.18: 4 residues within 4Å: Chain B: H.563, D.574, H.796, H.800 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.563, B:D.574, B:H.796, B:H.800

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W. et al., Structural insights into cholesterol transport and hydrolase activity of a putative human RNA transport protein SIDT1. Cell Discov (2024)

Release Date

2024-03-20

Peptides

SID1 transmembrane family member 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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SID1 transmembrane family member 1

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