SMTL ID : 8uvf.1

Structure of NaDC3-DMS complex in Ci-Ci conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: S.139, L.142, S.143, N.144, G.246, G.252 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.144 NA.2: 6 residues within 4Å: Chain A: T.479, A.482, S.483, N.484, A.520, S.526 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.526 NA.12: 6 residues within 4Å: Chain B: S.139, L.142, S.143, N.144, G.246, G.252 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.142 NA.13: 6 residues within 4Å: Chain B: T.479, A.482, S.483, N.484, A.520, S.526 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.482

6 x C14: TETRADECANE(Non-covalent)

C14.3: 6 residues within 4Å: Chain A: L.28, V.31, F.43, Y.51, L.69 Ligands: C14.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.28, A:V.31, A:F.43, A:Y.51, A:L.69 C14.4: 4 residues within 4Å: Chain A: R.40, F.72 Chain B: A.384 Ligands: C14.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.72, B:A.384 C14.11: 8 residues within 4Å: Chain A: F.340, Q.343, A.344, I.347, L.348, M.351, F.392, R.396 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.340, A:F.340, A:Q.343, A:I.347, A:L.348, A:F.392, A:F.392 C14.14: 6 residues within 4Å: Chain B: L.28, V.31, F.43, Y.51, L.69 Ligands: C14.15 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.28, B:V.31, B:F.43, B:Y.51, B:L.69 C14.15: 4 residues within 4Å: Chain A: A.384 Chain B: R.40, F.72 Ligands: C14.14 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.384, B:F.72 C14.22: 8 residues within 4Å: Chain B: F.340, Q.343, A.344, I.347, L.348, M.351, F.392, R.396 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.340, B:F.340, B:Q.343, B:I.347, B:L.348, B:F.392, B:F.392

4 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.5: 14 residues within 4Å: Chain A: A.33, L.34, L.42, I.45, L.46, V.50, C.53, T.54, W.451, Q.455, F.478, I.490, V.494 Ligands: CLR.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.45, A:L.46, A:V.50, A:T.54, A:F.478, A:V.494 Hydrogen bonds: A:Q.455 3PE.9: 11 residues within 4Å: Chain A: L.108, K.115, Y.332, I.338, Q.343, F.346, I.347, F.349, C.350, A.353, I.354 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.108, A:I.338, A:Q.343, A:F.346, A:F.346, A:F.346, A:F.346, A:I.347, A:F.349, A:A.353 Hydrogen bonds: A:Y.332 Salt bridges: A:K.115 3PE.16: 14 residues within 4Å: Chain B: A.33, L.34, L.42, I.45, L.46, V.50, C.53, T.54, W.451, Q.455, F.478, I.490, V.494 Ligands: CLR.17 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.45, B:L.46, B:V.50, B:T.54, B:F.478, B:V.494 Hydrogen bonds: B:Q.455 3PE.20: 11 residues within 4Å: Chain B: L.108, K.115, Y.332, I.338, Q.343, F.346, I.347, F.349, C.350, A.353, I.354 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.108, B:I.338, B:Q.343, B:F.346, B:F.346, B:F.346, B:F.346, B:I.347, B:F.349, B:A.353 Hydrogen bonds: B:Y.332 Salt bridges: B:K.115

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 7 residues within 4Å: Chain A: T.23, A.26, L.27, P.29, V.30, V.50 Ligands: 3PE.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.23, A:A.26, A:L.27, A:P.29, A:V.30, A:V.50 CLR.7: 5 residues within 4Å: Chain A: L.557, L.558, S.560, L.561, N.564 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.558, A:L.561, A:L.561, A:L.561 CLR.8: 7 residues within 4Å: Chain A: M.351, I.354, T.358, P.365, G.366, W.367, L.370 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.354, A:L.370 CLR.10: 10 residues within 4Å: Chain A: P.397, S.398, W.401, W.402, T.410, T.412 Chain B: A.14, L.17, L.21, F.22 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.401, B:L.17, B:L.17, B:L.21, B:F.22 Hydrogen bonds: A:T.410, A:T.410 CLR.17: 7 residues within 4Å: Chain B: T.23, A.26, L.27, P.29, V.30, V.50 Ligands: 3PE.16 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.23, B:A.26, B:L.27, B:P.29, B:V.30, B:V.50 CLR.18: 5 residues within 4Å: Chain B: L.557, L.558, S.560, L.561, N.564 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.558, B:L.561, B:L.561, B:L.561 CLR.19: 7 residues within 4Å: Chain B: M.351, I.354, T.358, P.365, G.366, W.367, L.370 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.354, B:L.370 CLR.21: 10 residues within 4Å: Chain A: A.14, L.17, L.21, F.22 Chain B: P.397, S.398, W.401, W.402, T.410, T.412 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.17, A:L.17, A:L.21, A:F.22, B:W.401 Hydrogen bonds: B:T.410, B:T.410

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Substrate translocation and inhibition in human dicarboxylate transporter NaDC3. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-12-25

Peptides

Na(+)/dicarboxylate cotransporter 3: 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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Na(+)/dicarboxylate cotransporter 3

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