SMTL ID : 8uvd.1

Structure of NaDC3-PF4a complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 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: XKC.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.139 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:T.479 NA.13: 7 residues within 4Å: Chain B: S.139, L.142, S.143, N.144, G.246, G.252 Ligands: XKC.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.252 NA.14: 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

2 x XKC: (2R)-2-hydroxy-2-[2-(2-methoxy-5-methylpyridin-3-yl)ethyl]butanedioic acid(Non-covalent)

XKC.3: 14 residues within 4Å: Chain A: L.59, S.143, N.144, T.145, G.252, T.253, I.429, L.432, S.483, N.484, T.485, T.527, P.528 Ligands: NA.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.59, A:I.429, A:L.432 Hydrogen bonds: A:N.144, A:T.145, A:T.145, A:T.145, A:N.484, A:T.527, A:T.527 XKC.15: 14 residues within 4Å: Chain B: L.59, S.143, N.144, T.145, G.252, T.253, I.429, L.432, S.483, N.484, T.485, T.527, P.528 Ligands: NA.13 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.59, B:I.429, B:L.432 Hydrogen bonds: B:N.144, B:T.145, B:T.145, B:T.145, B:N.484, B:T.527, B:T.527

6 x C14: TETRADECANE(Non-covalent)

C14.4: 5 residues within 4Å: Chain A: L.28, V.31, F.43, Y.51 Ligands: C14.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.28, A:V.31, A:F.43, A:Y.51 C14.5: 4 residues within 4Å: Chain A: R.40, F.72 Chain B: A.384 Ligands: C14.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.72, A:F.72, A:F.72, B:A.384 C14.12: 6 residues within 4Å: Chain A: F.340, Q.343, A.344, I.347, M.351, F.392 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.340, A:F.340, A:Q.343, A:A.344, A:I.347, A:F.392 C14.16: 5 residues within 4Å: Chain B: L.28, V.31, F.43, Y.51 Ligands: C14.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.28, B:V.31, B:F.43, B:Y.51 C14.17: 4 residues within 4Å: Chain A: A.384 Chain B: R.40, F.72 Ligands: C14.16 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.384, B:F.72, B:F.72, B:F.72 C14.24: 6 residues within 4Å: Chain B: F.340, Q.343, A.344, I.347, M.351, F.392 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.340, B:F.340, B:Q.343, B:A.344, B:I.347, B:F.392

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

3PE.6: 11 residues within 4Å: Chain A: L.34, L.42, I.45, L.46, C.53, T.54, W.451, Q.455, I.490, V.494 Ligands: CLR.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.45, A:L.46, A:L.46, A:T.54, A:Q.455, A:Q.455, A:V.494 3PE.10: 10 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 13 PLIP interactions: 13 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:F.346, A:I.347, A:F.349, A:A.353 Hydrogen bonds: A:Y.332 Salt bridges: A:K.115 3PE.18: 11 residues within 4Å: Chain B: L.34, L.42, I.45, L.46, C.53, T.54, W.451, Q.455, I.490, V.494 Ligands: CLR.19 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.45, B:L.46, B:L.46, B:T.54, B:Q.455, B:Q.455, B:V.494 3PE.22: 10 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 13 PLIP interactions: 13 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: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.7: 6 residues within 4Å: Chain A: A.26, L.27, P.29, V.30, V.50 Ligands: 3PE.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.27, A:P.29, A:P.29, A:V.30, A:V.50 CLR.8: 5 residues within 4Å: Chain A: L.557, L.558, S.560, L.561, N.564 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.558, A:L.561, A:L.561 CLR.9: 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:I.354, A:L.370, A:L.370 CLR.11: 9 residues within 4Å: Chain A: S.398, W.401, W.402, T.410, T.412 Chain B: A.14, L.17, L.21, F.22 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.14, B:L.17, B:L.17, B:L.21, B:F.22, A:W.401 Hydrogen bonds: A:T.410, A:T.410 CLR.19: 6 residues within 4Å: Chain B: A.26, L.27, P.29, V.30, V.50 Ligands: 3PE.18 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.27, B:P.29, B:P.29, B:V.30, B:V.50 CLR.20: 5 residues within 4Å: Chain B: L.557, L.558, S.560, L.561, N.564 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.558, B:L.561, B:L.561 CLR.21: 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:I.354, B:L.370, B:L.370 CLR.23: 9 residues within 4Å: Chain A: A.14, L.17, L.21, F.22 Chain B: S.398, W.401, W.402, T.410, T.412 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.14, 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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