SMTL ID : 8wor.1

Cryo-EM structure of human SIDT1 protein with C2 symmetry at neutral 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: 5 residues within 4Å: Chain A: V.55, N.57, S.59, T.60, L.155 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.83, E.124, L.162 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: V.55, N.57, S.59, T.60, L.155 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.83, E.124, L.162 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: H.563, H.796, H.800 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.563, A:H.796, A:H.800, H2O.1 ZN.18: 4 residues within 4Å: Chain B: S.559, H.563, H.796, H.800 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.563, B:H.796, B:H.800, H2O.1

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 3 residues within 4Å: Chain A: N.219, M.221, P.223 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:M.221, A:P.223 CA.19: 3 residues within 4Å: Chain B: N.219, M.221, P.223 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:M.221, B:P.223

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

NAG.7: 3 residues within 4Å: Chain A: F.40, N.67, L.144 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.40, A:L.144 NAG.8: 1 residues within 4Å: Chain A: N.136 No protein-ligand interaction detected (PLIP) NAG.20: 4 residues within 4Å: Chain B: F.40, N.67, Q.142, L.144 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.40, B:L.144 NAG.21: 1 residues within 4Å: Chain B: N.136 No protein-ligand interaction detected (PLIP)

15 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 6 residues within 4Å: Chain A: G.323, C.324, R.517, R.518, F.809, L.812 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.518, A:F.809, A:F.809, A:L.812 CLR.10: 4 residues within 4Å: Chain A: S.310, L.489, L.499 Ligands: OLA.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.489, A:L.499 CLR.11: 3 residues within 4Å: Chain A: A.760, Y.764 Ligands: CLR.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.760, A:Y.764, A:Y.764 CLR.12: 1 residues within 4Å: Chain A: Y.764 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.764 CLR.13: 6 residues within 4Å: Chain A: I.464, V.491, L.492, V.557, C.561 Ligands: CLR.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.464, A:V.491, A:L.492, A:V.557 CLR.14: 13 residues within 4Å: Chain A: F.702, F.705, R.712, D.713, S.716, Y.717, G.720, I.721, C.724, L.763, F.766 Ligands: CLR.11, SPL.16 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.702, A:F.702, A:F.705, A:F.705, A:D.713, A:Y.717, A:Y.717, A:L.763, A:F.766 CLR.17: 3 residues within 4Å: Chain A: V.620 Chain B: I.460 Ligands: CLR.29 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.460, A:V.620 CLR.22: 3 residues within 4Å: Chain A: I.460 Chain B: V.620 Ligands: CLR.13 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.460, B:V.620 CLR.23: 8 residues within 4Å: Chain A: Y.466, V.469, I.478, Y.480, P.777 Chain B: Y.466, V.469, I.478 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.466, A:V.469, A:I.478, A:P.777, B:Y.466, B:V.469, B:V.469, B:I.478 CLR.25: 6 residues within 4Å: Chain B: G.323, C.324, R.517, R.518, F.809, L.812 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.518, B:F.809, B:F.809, B:L.812 CLR.26: 4 residues within 4Å: Chain B: S.310, L.489, L.499 Ligands: OLA.31 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.489, B:L.499 CLR.27: 5 residues within 4Å: Chain B: W.759, A.760, L.763, Y.764 Ligands: CLR.30 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.759, B:L.763, B:Y.764, B:Y.764 CLR.28: 1 residues within 4Å: Chain B: Y.764 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.764 CLR.29: 6 residues within 4Å: Chain B: I.464, V.491, L.492, V.557, C.561 Ligands: CLR.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.464, B:V.491, B:L.492, B:V.557 CLR.30: 13 residues within 4Å: Chain B: F.702, F.705, R.712, D.713, S.716, Y.717, G.720, I.721, C.724, L.763, F.766 Ligands: SPL.24, CLR.27 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.702, B:F.702, B:F.705, B:F.705, B:D.713, B:Y.717, B:Y.717, B:L.763, B:F.766, B:F.766

2 x OLA: OLEIC ACID(Non-covalent)

OLA.15: 7 residues within 4Å: Chain A: L.489, L.502, V.505, G.556, V.557, A.560 Ligands: CLR.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.502, A:V.505, A:A.560 OLA.31: 7 residues within 4Å: Chain B: L.489, L.502, V.505, G.556, V.557, A.560 Ligands: CLR.26 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.502, B:V.505, B:A.560

2 x SPL: OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE(Non-covalent)

SPL.16: 10 residues within 4Å: Chain A: M.548, E.555, M.578, S.716, G.720, I.723, W.759, W.799, L.807 Ligands: CLR.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.723, A:W.759 Water bridges: A:S.803, A:S.803 SPL.24: 11 residues within 4Å: Chain B: M.548, E.555, M.578, S.716, G.720, I.723, L.727, W.759, W.799, L.807 Ligands: CLR.30 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.723, B:I.723, B:L.727, B:W.759 Water bridges: B:H.796, B:H.800, B:S.803, B:S.803

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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