SMTL ID : 2nwx.1

Crystal structure of GltPh in complex with L-aspartate and sodium ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

homo-trimer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: T.308, M.311, S.349, I.350, T.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.350 NA.2: 6 residues within 4Å: Chain A: S.278, G.306, A.307, N.310, N.401, D.405 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.278, A:G.306 NA.7: 6 residues within 4Å: Chain B: T.308, M.311, S.349, I.350, G.351, T.352 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.350 NA.8: 7 residues within 4Å: Chain B: S.278, G.306, A.307, N.310, M.311, N.401, D.405 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.278, B:D.405 NA.10: 6 residues within 4Å: Chain C: T.308, M.311, S.349, I.350, G.351, T.352 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.351 NA.11: 8 residues within 4Å: Chain C: S.278, G.306, A.307, N.310, M.311, N.401, V.402, D.405 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.278, C:N.401

3 x ASP: ASPARTIC ACID(Non-covalent)

ASP.3: 16 residues within 4Å: Chain A: R.276, S.277, S.278, M.311, T.314, T.352, A.353, G.354, V.355, P.356, G.357, G.359, D.394, R.397, T.398, N.401 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.278, A:V.355, A:G.359, A:D.394, A:N.401, D.3, D.3 Salt bridges: A:R.397 ASP.4: 17 residues within 4Å: Chain B: R.276, S.277, S.278, M.311, T.314, T.352, A.353, G.354, V.355, P.356, G.357, A.358, G.359, D.394, R.397, T.398, N.401 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:S.278, B:T.314, B:V.355, B:G.359, B:D.394, B:N.401, D.4, D.4 Salt bridges: B:R.397 ASP.5: 16 residues within 4Å: Chain C: R.276, S.277, S.278, M.311, T.314, T.352, A.353, G.354, V.355, P.356, A.358, G.359, D.394, R.397, T.398, N.401 9 PLIP interactions: 7 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:S.278, C:T.314, C:V.355, C:G.359, C:D.394, C:N.401, D.5, D.5 Salt bridges: C:R.397

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.6: 2 residues within 4Å: Chain A: I.350, G.351 No protein-ligand interaction detected (PLIP) PLM.9: 6 residues within 4Å: Chain B: I.133, I.137, L.152, I.309, I.350, G.351 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.133, B:I.137, B:L.152, B:I.309 PLM.12: 6 residues within 4Å: Chain C: I.133, L.134, I.137, L.347, I.350, G.351 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.133, C:L.134, C:I.137, C:L.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boudker, O. et al., Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Nature (2007)

Release Date

2007-02-27

Peptides

425aa long hypothetical proton glutamate symport protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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425aa long hypothetical proton glutamate symport protein

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