SMTL ID : 7oix.1

Structure of thermostable human MFSD2A in complex with thermostable human Sync2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 11 residues within 4Å: Chain A: K.174, N.177, R.203, F.205, W.206, R.208, D.211, Y.212, N.213, Q.232, T.233 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.213, A:N.213, A:R.203, A:K.174, A:R.208, A:N.213

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.2: 12 residues within 4Å: Chain A: R.131, N.133, Q.156, Y.158, R.171, P.173, T.264, S.265, I.269, L.280, H.287, N.312 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.173 Hydrogen bonds: A:Q.156

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

NAG.3: 3 residues within 4Å: Chain A: I.122, N.146, L.221 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: K.132, N.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.133 NAG.5: 4 residues within 4Å: Chain A: N.146, G.183, T.184, N.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.220 NAG.6: 2 residues within 4Å: Chain A: N.247 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.247 NAG.7: 5 residues within 4Å: Chain A: E.226, W.239, N.241, T.243 Ligands: NAG.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Molledo, M. et al., Structural insights into the lysophospholipid brain uptake mechanism and its inhibition by syncytin-2. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-06-01

Peptides

Syncytin-2: A
Isoform 2 of Sodium-dependent lysophosphatidylcholine symporter 1: B

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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Syncytin-2

Isoform 2 of Sodium-dependent lysophosphatidylcholine symporter 1