SMTL ID : 8d2t.1

Zebrafish MFSD2A isoform B in inward open ligand-free conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

10 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 6 residues within 4Å: Chain A: Y.74, V.81, Q.134, L.141 Ligands: LMT.8, LMT.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.81, A:L.141 Hydrogen bonds: A:Q.134 LMT.2: 4 residues within 4Å: Chain A: L.188, Q.196, N.327, L.330 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.188, A:Q.196, A:L.330 LMT.3: 7 residues within 4Å: Chain A: I.193, I.197, D.234, I.241, V.245, I.249 Ligands: LMT.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.193, A:I.197, A:V.245, A:V.245, A:I.249 Hydrogen bonds: A:D.234, A:N.237 LMT.4: 7 residues within 4Å: Chain A: F.124, Q.233, N.237, M.240, I.241 Ligands: LMT.3, LMT.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.124, A:I.241 Hydrogen bonds: A:Q.233, A:Q.233 LMT.5: 6 residues within 4Å: Chain A: F.124, Y.128, G.244, C.247 Ligands: LMT.4, LMT.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.124 LMT.6: 11 residues within 4Å: Chain A: L.121, F.124, L.125, Y.128, P.130, S.131, V.132, D.133, W.139 Ligands: LMT.5, LMT.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.121, A:F.124, A:F.124, A:F.124, A:L.125, A:Y.128 Hydrogen bonds: A:Y.128, A:S.131, A:S.131, A:D.133 LMT.7: 10 residues within 4Å: Chain A: S.438, V.441, S.445, F.448, E.461, L.464, T.465, I.468, L.469, A.473 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.441, A:T.465, A:I.468, A:L.469, A:A.473 LMT.8: 8 residues within 4Å: Chain A: V.132, Q.134, G.135, V.138, W.139, F.143 Ligands: LMT.1, LMT.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.139, A:W.139, A:F.143 Hydrogen bonds: A:Q.134 LMT.9: 7 residues within 4Å: Chain A: L.40, A.177, Y.178, T.181, V.182, L.185, V.252 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.185, A:V.252 Hydrogen bonds: A:Y.178, A:T.181 LMT.10: 9 residues within 4Å: Chain A: D.71, F.73, Y.74, I.77 Chain B: Y.48 Chain C: L.97, F.102, P.104 Ligands: LMT.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.77 Hydrogen bonds: B:K.54, B:K.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, C. et al., Lipid flipping in the omega-3 fatty-acid transporter. Nat Commun (2023)

Release Date

2023-05-10

Peptides

Sodium-dependent lysophosphatidylcholine symporter 1-B: A
FAB light chain: B
FAB heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

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

Sodium-dependent lysophosphatidylcholine symporter 1-B

FAB light chain

FAB heavy chain

Related Entries With Identical Sequence