SMTL ID : 8uvc.1

Structure of NaDC3-aKG complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

NA.1: 7 residues within 4Å: Chain A: S.139, L.142, S.143, N.144, G.246, G.252 Ligands: AKG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.139 NA.13: 7 residues within 4Å: Chain B: S.139, L.142, S.143, N.144, G.246, G.252 Ligands: AKG.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.139

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 12 residues within 4Å: Chain A: S.143, N.144, G.252, T.253, A.254, P.255, S.483, N.484, T.485, T.527, P.528 Ligands: NA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.144, A:N.144, A:A.254, A:N.484, A:T.485, A:T.527, A:T.527 AKG.14: 12 residues within 4Å: Chain B: S.143, N.144, G.252, T.253, A.254, P.255, S.483, N.484, T.485, T.527, P.528 Ligands: NA.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.144, B:N.144, B:A.254, B:N.484, B:T.485, B:T.527, B:T.527

6 x C14: TETRADECANE(Non-covalent)

C14.3: 6 residues within 4Å: Chain A: L.28, F.43, Y.51, L.69, M.73 Ligands: C14.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.28, A:F.43, A:L.69 C14.4: 4 residues within 4Å: Chain A: F.72 Chain B: N.372, A.384 Ligands: C14.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.72, A:F.72, B:A.384 C14.11: 7 residues within 4Å: Chain A: F.340, Q.343, A.344, I.347, M.351, F.392, R.396 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.340, A:A.344, A:I.347, A:I.347, A:F.392, A:F.392 C14.12: 4 residues within 4Å: Chain A: N.372, A.384 Chain B: F.72 Ligands: C14.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.72, B:F.72, A:A.384 C14.15: 6 residues within 4Å: Chain B: L.28, F.43, Y.51, L.69, M.73 Ligands: C14.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.28, B:F.43, B:L.69 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:A.344, B:I.347, B:I.347, B:F.392, B:F.392

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

3PE.5: 10 residues within 4Å: Chain A: L.34, L.42, I.45, L.46, T.54, W.451, Q.455, I.490, V.494 Ligands: CLR.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.45, A:L.46, A:L.46, A:T.54, A:W.451, A:Q.455, A:Q.455, A:V.494 3PE.9: 11 residues within 4Å: Chain A: L.108, R.111, I.112, K.115, Y.332, I.338, F.346, I.347, C.350, A.353, I.354 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.108, A:I.112, A:F.346, A:F.346, A:I.347, A:A.353, A:I.354 Hydrogen bonds: A:Y.332 Salt bridges: A:K.115 3PE.16: 10 residues within 4Å: Chain B: L.34, L.42, I.45, L.46, T.54, W.451, Q.455, I.490, V.494 Ligands: CLR.17 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.45, B:L.46, B:L.46, B:T.54, B:W.451, B:Q.455, B:Q.455, B:V.494 3PE.20: 11 residues within 4Å: Chain B: L.108, R.111, I.112, K.115, Y.332, I.338, F.346, I.347, C.350, A.353, I.354 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.108, B:I.112, B:F.346, B:F.346, B:I.347, B:A.353, B:I.354 Hydrogen bonds: B:Y.332 Salt bridges: B:K.115

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 6 residues within 4Å: Chain A: A.26, L.27, P.29, V.30, V.50 Ligands: 3PE.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.27, A:V.30, A:V.50 CLR.7: 5 residues within 4Å: Chain A: A.465, L.557, S.560, L.561, N.564 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.465, A:L.557, A:L.557, A:L.561, A:L.561, A:N.564 CLR.8: 7 residues within 4Å: Chain A: M.351, I.354, T.358, P.365, G.366, W.367, L.370 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.351, A:I.354, A:L.370 CLR.10: 9 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 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.401, A:W.402, B:L.17, B:L.17, B:L.21 Hydrogen bonds: A:T.410, A:T.410 CLR.17: 6 residues within 4Å: Chain B: A.26, L.27, P.29, V.30, V.50 Ligands: 3PE.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.27, B:V.30, B:V.50 CLR.18: 5 residues within 4Å: Chain B: A.465, L.557, S.560, L.561, N.564 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.465, B:L.557, B:L.557, B:L.561, B:L.561, B:N.564 CLR.19: 7 residues within 4Å: Chain B: M.351, I.354, T.358, P.365, G.366, W.367, L.370 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:M.351, B:I.354, B:L.370 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 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.401, B:W.402, A:L.17, A:L.17, A:L.21 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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