SMTL ID : 8w6d.1

CryoEM structure of NaDC1 in apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: S.149, I.152, S.153, N.154, G.252 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.154 NA.4: 5 residues within 4Å: Chain B: S.149, I.152, S.153, N.154, G.252 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.152

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

3PH.2: 13 residues within 4Å: Chain A: L.118, R.121, I.122, R.125, V.126, I.129, V.130, G.140, F.141, V.144, H.332, S.346, F.349 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.125, A:V.126, A:I.129, A:V.130, A:F.141, A:V.144, A:V.144, A:F.349 Salt bridges: A:R.121, A:R.125, A:H.332 3PH.5: 13 residues within 4Å: Chain B: L.118, R.121, I.122, R.125, V.126, I.129, V.130, G.140, F.141, V.144, H.332, S.346, F.349 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.125, B:V.126, B:I.129, B:V.130, B:F.141, B:V.144, B:V.144, B:F.349 Salt bridges: B:R.121, B:R.125, B:H.332

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 8 residues within 4Å: Chain A: Y.50, Y.53, L.57, F.75, L.79, M.82 Chain B: I.392, I.393 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.53, A:L.57, A:F.75, A:L.79, B:I.392, B:I.393 Y01.6: 8 residues within 4Å: Chain A: I.392, I.393 Chain B: Y.50, Y.53, L.57, F.75, L.79, M.82 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.392, A:I.393, B:Y.53, B:L.57, B:F.75, B:L.79

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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