SMTL ID : 8uve.1

Structure of NaDC3-Succinate complex in Coo-Ci conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: T.479, A.482, S.483, N.484, A.520, S.526 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.479, A:A.482 NA.12: 5 residues within 4Å: Chain B: S.139, L.142, S.143, N.144, G.252 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.139

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 12 residues within 4Å: Chain A: F.93, S.143, N.144, T.145, T.253, P.255, L.433, S.483, N.484, T.485, T.527, P.528 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.93, A:L.433, A:P.528 Hydrogen bonds: A:N.144, A:N.144, A:T.145, A:T.145, A:T.145, A:T.253, A:N.484, A:N.484, A:T.485 SIN.13: 6 residues within 4Å: Chain B: N.144, G.252, T.253, N.484, T.527, P.528 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.527, B:T.527

6 x C14: TETRADECANE(Non-covalent)

C14.3: 5 residues within 4Å: Chain A: L.28, F.43, L.69, M.73 Ligands: C14.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.28, A:F.43, A:F.43, A:L.69 C14.4: 4 residues within 4Å: Chain A: R.40, F.72, M.73 Ligands: C14.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.72 C14.10: 7 residues within 4Å: Chain A: F.340, Q.343, A.344, I.347, L.348, F.392, R.396 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.344, A:I.347, A:I.347, A:I.347, A:L.348, A:F.392, A:F.392 C14.14: 6 residues within 4Å: Chain B: L.20, L.28, F.43, Y.51, M.73 Ligands: C14.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.20, B:L.28, B:F.43 C14.15: 4 residues within 4Å: Chain B: R.40, V.68, F.72 Ligands: C14.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.68, B:F.72, B:F.72 C14.22: 7 residues within 4Å: Chain B: F.340, Q.343, A.344, I.347, M.351, F.392, R.396 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.340, B:Q.343, B:A.344, B:I.347, B:F.392, B:F.392

10 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 6 residues within 4Å: Chain A: T.23, A.26, L.27, P.29, V.30 Ligands: CLR.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.23, A:A.26, A:L.27, A:V.30 CLR.6: 7 residues within 4Å: Chain A: A.33, L.42, L.46, W.451, Q.455 Ligands: CLR.5, CLR.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.33, A:L.42, A:L.46, A:W.451 CLR.7: 6 residues within 4Å: Chain A: I.452, Q.455, L.456, F.478, F.491 Ligands: CLR.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.452, A:L.456, A:F.478, A:F.491 CLR.8: 6 residues within 4Å: Chain A: T.358, P.365, G.366, W.367, S.369, L.370 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.365, A:W.367, A:L.370 CLR.9: 9 residues within 4Å: Chain A: P.397, S.398, W.401, W.402, T.410, T.412 Chain B: A.14, L.17, F.22 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.397, A:W.401, A:T.412, B:A.14, B:L.17, B:F.22 Hydrogen bonds: A:T.410 CLR.11: 4 residues within 4Å: Chain A: I.112, K.115, L.119, T.134 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.112 CLR.17: 6 residues within 4Å: Chain B: A.26, L.27, P.29, V.30, V.50 Ligands: 3PE.16 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.29, B:P.29, B:V.30, B:V.50 CLR.18: 4 residues within 4Å: Chain B: L.557, S.560, L.561, N.564 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.557, B:L.557, B:L.557, B:L.561, B:L.561 CLR.19: 6 residues within 4Å: Chain B: M.351, I.354, T.358, P.365, G.366, W.367 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.354 CLR.21: 9 residues within 4Å: Chain A: A.14, L.17, L.21 Chain B: P.397, S.398, W.401, W.402, T.410, T.412 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.401, B:W.401, B:W.402, A:A.14, A:L.17, A:L.17, A:L.21 Hydrogen bonds: B:T.410, B:T.410

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

3PE.16: 12 residues within 4Å: Chain B: L.34, I.45, L.46, A.49, C.53, T.54, W.451, Q.455, F.478, I.490, V.494 Ligands: CLR.17 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.45, B:L.46, B:L.46, B:A.49, B:T.54, B:Q.455, B:Q.455, B:F.478, B:V.494 3PE.20: 9 residues within 4Å: Chain B: L.108, K.115, Y.332, I.338, F.346, I.347, F.349, C.350, A.353 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.108, B:I.338, B:F.346, 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

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
B

B
A

Membrane

We predict this structure to be a membrane protein.
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Na(+)/dicarboxylate cotransporter 3

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