SMTL ID : 8uvg.1

Structure of NaDC3-DMS complex in Co-Ci conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

1 x XKH: (2R,3S)-2,3-dimethylbutanedioic acid(Non-covalent)

XKH.1: 10 residues within 4Å: Chain A: S.143, N.144, T.145, A.254, P.255, N.484, T.485, T.527, P.528, P.529 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.144 Hydrogen bonds: A:N.144, A:N.144, A:T.145, A:A.254, A:N.484, A:T.485

7 x C14: TETRADECANE(Non-covalent)

C14.2: 4 residues within 4Å: Chain A: V.31, F.43, Y.51 Ligands: C14.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.31, A:F.43, A:F.43 C14.3: 5 residues within 4Å: Chain A: R.40, F.72, M.73 Chain B: N.372 Ligands: C14.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.72, A:M.73 C14.7: 3 residues within 4Å: Chain A: W.141, F.275, F.363 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.141, A:W.141, A:F.275, A:F.275, A:F.363 C14.10: 6 residues within 4Å: Chain A: F.340, Q.343, I.347, L.348, M.351, F.392 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 C14.13: 4 residues within 4Å: Chain B: L.28, Y.51, M.73 Ligands: C14.14 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.28 C14.14: 3 residues within 4Å: Chain B: R.40, F.72 Ligands: C14.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.72 C14.21: 4 residues within 4Å: Chain B: F.340, Q.343, I.347, F.392 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.340, B:Q.343, B:I.347, B:F.392

9 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 7 residues within 4Å: Chain A: T.23, A.26, L.27, P.29, V.30, V.50 Ligands: CLR.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.23, A:L.27, A:P.29 CLR.5: 5 residues within 4Å: Chain A: A.33, L.46, W.451 Ligands: CLR.4, CLR.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.33, A:L.46, A:W.451 CLR.6: 10 residues within 4Å: Chain A: L.42, I.45, L.46, I.452, Q.455, L.456, P.458, F.478, F.481 Ligands: CLR.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.42, A:L.46, A:I.452, A:I.452, A:Q.455, A:F.478, A:F.481, A:F.481 CLR.8: 6 residues within 4Å: Chain A: I.354, T.358, P.365, G.366, W.367, S.369 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.354, A:T.358, A:W.367 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, L.21 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.401, A:W.401, A:W.402, A:T.412, B:A.14, B:L.17 Hydrogen bonds: A:T.410 CLR.16: 5 residues within 4Å: Chain B: T.23, A.26, L.27, P.29 Ligands: 3PE.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.26, B:L.27, B:P.29 CLR.17: 4 residues within 4Å: Chain B: L.557, S.560, L.561, N.564 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.557, B:L.561, B:L.561 CLR.18: 5 residues within 4Å: Chain B: I.354, L.355, I.364, P.365, W.367 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.354, B:L.355, B:I.364, B:P.365, B:W.367 CLR.20: 9 residues within 4Å: Chain A: A.14, L.17, L.18 Chain B: P.397, S.398, W.401, W.402, T.410, T.412 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.14, A:L.17, A:L.18, B:P.397, B:W.401, B:W.401, B:W.402 Hydrogen bonds: B:T.410, B:T.410

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

NA.11: 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 NA.12: 7 residues within 4Å: Chain B: T.479, A.482, S.483, N.484, A.520, S.526, T.527 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.479

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

3PE.15: 11 residues within 4Å: Chain B: L.34, I.45, L.46, C.53, T.54, W.451, Q.455, F.478, I.490, V.494 Ligands: CLR.16 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.45, B:L.46, B:Q.455, B:Q.455, B:F.478, B:V.494 3PE.19: 10 residues within 4Å: Chain B: L.108, K.115, Y.332, I.338, Q.343, F.346, I.347, C.350, A.353, I.354 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.108, B:Q.343, B:F.346, B:I.347, B:A.353, B:I.354, B:I.354 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.
Show / Hide

Na(+)/dicarboxylate cotransporter 3

Related Entries With Identical Sequence