SMTL ID : 8uvi.1

Structure of NaDC3-Succinate complex in Coo-Coo conformation

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: T.479, A.482, S.483, N.484, C.517, A.520, S.526 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.484 NA.12: 7 residues within 4Å: Chain B: T.479, A.482, S.483, N.484, C.517, A.520, S.526 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.517

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 11 residues within 4Å: Chain A: F.93, S.143, N.144, T.145, T.253, L.433, S.483, N.484, T.485, T.527, P.528 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.93, A:L.433, A:P.528 Hydrogen bonds: A:N.144, A:T.145, A:T.253, A:N.484, A:N.484, A:T.485, A:T.527, A:T.527 SIN.13: 11 residues within 4Å: Chain B: F.93, S.143, N.144, T.145, T.253, L.433, S.483, N.484, T.485, T.527, P.528 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.93, B:L.433, B:P.528 Hydrogen bonds: B:N.144, B:T.145, B:T.253, B:N.484, B:N.484, B:T.485, B:T.527, B:T.527

6 x C14: TETRADECANE(Non-covalent)

C14.3: 4 residues within 4Å: Chain A: F.43, L.69, M.73 Ligands: C14.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.43, A:L.69 C14.4: 4 residues within 4Å: Chain A: V.68, F.72 Chain B: A.384 Ligands: C14.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.68, A:F.72, A:F.72, A:F.72, B:A.384 C14.10: 8 residues within 4Å: Chain A: F.340, Q.343, A.344, I.347, L.348, M.351, F.392, R.396 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.340, A:I.347, A:L.348, A:F.392, A:F.392 C14.14: 4 residues within 4Å: Chain B: F.43, L.69, M.73 Ligands: C14.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.43, B:L.69 C14.15: 4 residues within 4Å: Chain A: A.384 Chain B: V.68, F.72 Ligands: C14.14 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.68, B:F.72, B:F.72, B:F.72, A:A.384 C14.21: 8 residues within 4Å: Chain B: F.340, Q.343, A.344, I.347, L.348, M.351, F.392, R.396 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.340, B:I.347, B:L.348, B:F.392, B:F.392

12 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 6 residues within 4Å: Chain A: A.26, L.27, P.29, V.30, V.50 Ligands: CLR.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.26, A:V.30, A:V.50 CLR.6: 5 residues within 4Å: Chain A: A.33, L.46, W.451 Ligands: CLR.5, CLR.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.33, A:L.46, A:W.451 CLR.7: 9 residues within 4Å: Chain A: L.42, I.45, L.448, I.452, Q.455, P.458, F.478, F.491 Ligands: CLR.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.42, A:L.448, A:I.452, A:Q.455, A:F.478, A:F.491 CLR.8: 8 residues within 4Å: Chain A: M.351, I.354, L.355, T.358, P.365, G.366, W.367, L.370 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.351, A:I.354, A:L.355, A:L.370 CLR.9: 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.18, L.21 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.401, B:L.17, B:L.17, B:L.18 CLR.11: 4 residues within 4Å: Chain A: I.112, K.115, L.119, T.134 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.112, A:L.119, A:L.119 CLR.16: 6 residues within 4Å: Chain B: A.26, L.27, P.29, V.30, V.50 Ligands: CLR.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.26, B:V.30, B:V.50 CLR.17: 5 residues within 4Å: Chain B: A.33, L.46, W.451 Ligands: CLR.16, CLR.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.33, B:L.46, B:W.451 CLR.18: 9 residues within 4Å: Chain B: L.42, I.45, L.448, I.452, Q.455, P.458, F.478, F.491 Ligands: CLR.17 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.42, B:L.448, B:I.452, B:Q.455, B:F.478, B:F.491 CLR.19: 8 residues within 4Å: Chain B: M.351, I.354, L.355, T.358, P.365, G.366, W.367, L.370 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:M.351, B:I.354, B:L.355, B:L.370 CLR.20: 10 residues within 4Å: Chain A: A.14, L.17, L.18, L.21 Chain B: P.397, S.398, W.401, W.402, T.410, T.412 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.14, A:L.17, A:L.17, A:L.18, B:W.401 CLR.22: 4 residues within 4Å: Chain B: I.112, K.115, L.119, T.134 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.112, B:L.119, B:L.119

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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