SMTL ID : 6ol1.2 (1 other biounit)

Structure of VcINDY in complex with Succinate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.09 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: T.360, A.363, S.364, N.365, A.401, A.407 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.365 NA.2: 5 residues within 4Å: Chain A: S.133, I.136, S.137, N.138, G.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.137 NA.4: 6 residues within 4Å: Chain B: T.360, A.363, S.364, N.365, A.401, A.407 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.407 NA.5: 7 residues within 4Å: Chain B: S.133, M.134, W.135, I.136, S.137, N.138, G.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.186

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.3: 11 residues within 4Å: Chain A: S.137, N.138, T.139, G.186, S.187, P.188, S.364, N.365, T.366, T.408, P.409 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.408 Hydrogen bonds: A:N.138, A:T.139, A:S.187, A:N.365, A:T.366, A:A.407 SIN.6: 12 residues within 4Å: Chain B: S.137, N.138, T.139, G.186, S.187, P.188, P.189, S.364, N.365, T.366, T.408, P.409 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:N.365, B:T.366 Hydrogen bonds: B:N.138, B:T.139, B:T.139, B:S.187, B:N.365, B:T.366, B:T.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klinz-Thompson, C.D. et al., Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter. Biorxiv (2022)

Release Date

2020-10-28

Peptides

Transporter, NadC family: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Membrane

We predict this structure to be a membrane protein.
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Transporter, NadC family

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