SMTL ID : 8w6c.1

CryoEM structure of NaDC1 with Citrate

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.149, I.152, S.153, N.154, G.246, G.252 Ligands: CIT.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.149 NA.2: 5 residues within 4Å: Chain A: T.484, T.487, S.488, N.489, A.531 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.484 NA.8: 7 residues within 4Å: Chain B: S.149, I.152, S.153, N.154, G.246, G.252 Ligands: CIT.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.154 NA.9: 5 residues within 4Å: Chain B: T.484, T.487, S.488, N.489, A.531 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.484

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 13 residues within 4Å: Chain A: L.38, K.47, Y.50, Y.53, L.57, F.75, I.78, L.79, M.82, M.83 Chain B: F.389, I.392, I.393 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.38, A:Y.50, A:Y.53, A:L.57, A:F.75, A:I.78, A:L.79, B:F.389, B:I.393 Hydrogen bonds: A:Y.50 Salt bridges: A:K.47 Y01.5: 12 residues within 4Å: Chain A: F.389, I.392, I.396 Chain B: L.38, K.47, Y.50, Y.53, L.57, I.78, L.79, M.82, M.83 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.389, A:F.389, A:I.392, A:I.396, B:L.38, B:Y.50, B:Y.53, B:L.57, B:I.78, B:L.79 Hydrogen bonds: B:Y.50 Salt bridges: B:K.47

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 10 residues within 4Å: Chain A: S.153, N.154, T.155, T.251, G.252, T.253, A.254, N.489, T.532 Ligands: NA.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.153, A:N.154, A:N.154, A:T.155, A:T.155, A:G.252, A:A.254, A:N.489 CIT.10: 10 residues within 4Å: Chain B: S.153, N.154, T.155, T.251, G.252, T.253, A.254, N.489, T.532 Ligands: NA.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.153, B:N.154, B:N.154, B:T.155, B:T.155, B:G.252, B:A.254, B:N.489

2 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.6: 14 residues within 4Å: Chain A: R.121, I.122, R.125, V.126, I.129, V.130, G.140, F.141, V.144, M.161, I.164, H.332, S.346, F.349 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.122, A:V.126, A:I.129, A:V.130, A:F.141, A:V.144, A:I.164, A:F.349 Salt bridges: A:R.121, A:R.125, A:H.332 3PH.7: 13 residues within 4Å: Chain B: R.121, R.125, V.126, I.129, V.130, G.140, F.141, V.144, M.161, I.164, H.332, S.346, F.349 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.129, B:V.130, B:F.141, B:V.144, B:I.164, B:F.349 Salt bridges: B:R.121, B:R.125, B:H.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chi, X. et al., Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism. Sci Adv (2024)

Release Date

2024-04-17

Peptides

Solute carrier family 13 member 2: 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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Solute carrier family 13 member 2

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