SMTL ID : 8kcx.1

Cryo-EM structure of human SIDT1

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: Y.81, N.83, E.124, L.162, Q.288 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: Y.81, N.83, E.124, L.162, Q.288 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 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: V.55, N.57, S.59, T.60, L.155 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.67, Q.142, L.144 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: V.55, N.57, S.59, T.60, L.155 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.9: 3 residues within 4Å: Chain A: H.563, H.791, H.795 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.563, A:H.791, A:H.795 ZN.10: 3 residues within 4Å: Chain B: H.563, H.791, H.795 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.563, B:H.791, B:H.795

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.
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SID1 transmembrane family member 1

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