SMTL ID : 8d2s.1

Zebrafish MFSD2A isoform B in inward open ligand bound conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

3 x ZGS: [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (9~{Z},12~{Z},15~{Z})-octadeca-9,12,15-trienoate(Non-covalent)

ZGS.1: 24 residues within 4Å: Chain A: Q.50, F.58, R.83, D.86, E.183, F.304, M.305, L.307, E.308, F.311, M.333, A.383, A.387, V.391, F.395, W.399, Y.424, Y.427, V.428, T.431, K.432, S.435 Ligands: ZGS.2, NA.21 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.58, A:L.307, A:F.311, A:F.311, A:A.387, A:V.391, A:F.395, A:F.395 Water bridges: A:Y.424 Salt bridges: A:D.86, A:K.432 ZGS.2: 21 residues within 4Å: Chain A: S.159, R.179, M.180, E.183, V.184, T.187, L.188, M.333, A.336, T.337, I.340, V.391, A.392, F.395, W.399, L.402, E.420, Y.424 Ligands: ZGS.1, ZGS.3, NA.21 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:M.180, A:V.184, A:V.184, A:T.187, A:L.188, A:M.333, A:A.336, A:I.340, A:V.391, A:F.395, A:W.399 Hydrogen bonds: A:S.159, A:R.179 Water bridges: A:Y.424 Salt bridges: A:E.420 ZGS.3: 14 residues within 4Å: Chain A: D.173, T.181, V.184, L.334, T.337, L.338, I.340, Q.344, L.396, W.399, P.403, V.406, E.420 Ligands: ZGS.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.181, A:V.184, A:L.338, A:L.396 Hydrogen bonds: A:Q.344, A:W.399 Salt bridges: A:E.420

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

LMT.4: 10 residues within 4Å: Chain A: L.188, I.189, A.192, Q.196, N.323, D.324, Q.326, N.327, L.330 Ligands: LMT.5 Ligand excluded by PLIP LMT.5: 7 residues within 4Å: Chain A: I.189, I.193, Q.196, I.197, M.200 Ligands: LMT.4, LMT.6 Ligand excluded by PLIP LMT.6: 11 residues within 4Å: Chain A: I.193, I.197, A.201, D.234, A.238, I.241, V.245, I.249 Ligands: LMT.5, LMT.10, LMT.11 Ligand excluded by PLIP LMT.7: 10 residues within 4Å: Chain A: V.120, L.121, F.124, L.125, Y.128, P.130, S.131, V.132, W.139 Ligands: LMT.15 Ligand excluded by PLIP LMT.8: 12 residues within 4Å: Chain A: D.71, F.73, Y.74, I.77, F.80, V.81 Chain B: Y.48, K.54 Chain C: L.97, F.102, P.104 Ligands: LMT.17 Ligand excluded by PLIP LMT.9: 11 residues within 4Å: Chain A: S.438, V.441, S.442, S.445, F.448, E.461, L.464, T.465, I.468, L.469, A.473 Ligand excluded by PLIP LMT.10: 15 residues within 4Å: Chain A: K.39, L.40, A.47, I.51, S.174, A.177, Y.178, T.181, V.182, L.185, I.189, I.249 Ligands: LMT.6, LMT.11, LMT.20 Ligand excluded by PLIP LMT.11: 5 residues within 4Å: Chain A: V.36, L.40, Y.178 Ligands: LMT.6, LMT.10 Ligand excluded by PLIP LMT.12: 7 residues within 4Å: Chain A: C.37, S.38, C.41, V.255, V.256, L.259, G.260 Ligand excluded by PLIP LMT.13: 8 residues within 4Å: Chain A: P.101, W.102, T.103, W.111, L.114, S.115, L.150 Ligands: LMT.14 Ligand excluded by PLIP LMT.14: 9 residues within 4Å: Chain A: L.96, R.99, T.100, P.101, W.111, T.149, L.150, C.153 Ligands: LMT.13 Ligand excluded by PLIP LMT.15: 7 residues within 4Å: Chain A: L.125, Q.134, G.135, V.138, W.139, F.143 Ligands: LMT.7 Ligand excluded by PLIP LMT.16: 10 residues within 4Å: Chain A: Y.128, S.131, Q.233, N.237, M.240, I.241, G.244, V.245, A.248 Chain B: A.65 Ligand excluded by PLIP LMT.17: 6 residues within 4Å: Chain A: Y.74, G.135, V.137, L.141 Ligands: LMT.8, LMT.18 Ligand excluded by PLIP LMT.18: 6 residues within 4Å: Chain A: W.85, V.138, I.142, C.145, C.146 Ligands: LMT.17 Ligand excluded by PLIP LMT.19: 8 residues within 4Å: Chain A: I.368, V.371, G.460, K.463, L.464, K.467, S.471, I.475 Ligand excluded by PLIP LMT.20: 5 residues within 4Å: Chain A: C.37, L.40, I.44, V.252 Ligands: LMT.10 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.21: 5 residues within 4Å: Chain A: Y.49, Q.50, E.183 Ligands: ZGS.1, ZGS.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.183

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.
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Sodium-dependent lysophosphatidylcholine symporter 1-B

FAB light chain

FAB heavy chain

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