SMTL ID : 7o82.1

The L-arginine/agmatine antiporter from E. coli at 1.7 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

3 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.1: 7 residues within 4Å: Chain A: I.99, L.352, V.353, V.356, F.360, W.412, T.416 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.99, A:L.352, A:F.360 BNG.6: 9 residues within 4Å: Chain B: L.95, I.99, L.352, V.353, V.356, F.360, K.408, W.412, T.416 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.352, B:V.356 Hydrogen bonds: B:W.412 BNG.7: 4 residues within 4Å: Chain B: I.43, Y.44, M.179, W.182 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.44, B:W.182

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 6 residues within 4Å: Chain A: Y.87, L.309, F.310, P.311, N.427, Y.428 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.87, A:Y.87, A:Y.428, A:Y.428 TRS.8: 8 residues within 4Å: Chain B: Y.87, L.309, F.310, P.311, M.423, N.427, Y.428 Ligands: HEX.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.427 Water bridges: B:N.427, B:N.427

6 x HEX: HEXANE(Non-covalent)(Non-functional Binders)

HEX.3: 5 residues within 4Å: Chain A: L.12, I.13, T.16, I.226, G.230 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.12, A:I.13 HEX.9: 5 residues within 4Å: Chain B: P.311, I.313, F.314, I.329 Ligands: TRS.8 No protein-ligand interaction detected (PLIP) HEX.10: 6 residues within 4Å: Chain B: I.313, R.316, V.324, A.325, I.328, I.329 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.325, B:I.328 HEX.11: 5 residues within 4Å: Chain B: I.135, L.139, M.146, V.150 Ligands: D10.14 No protein-ligand interaction detected (PLIP) HEX.12: 5 residues within 4Å: Chain B: Y.44, L.47, V.48, T.189, I.193 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.44, B:Y.44 HEX.13: 1 residues within 4Å: Chain B: D.306 No protein-ligand interaction detected (PLIP)

2 x D10: DECANE(Non-covalent)

D10.4: 8 residues within 4Å: Chain A: M.146, R.149, V.150, V.153, A.154, L.157, A.284 Ligands: OCT.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.149, A:V.153 D10.14: 7 residues within 4Å: Chain B: M.146, R.149, V.150, V.153, A.154, L.157 Ligands: HEX.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.153, B:V.153

1 x OCT: N-OCTANE(Non-covalent)

OCT.5: 7 residues within 4Å: Chain A: I.135, F.136, L.139, M.146, V.150, L.287 Ligands: D10.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ilgu, H. et al., High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding. Bmc Biol. (2021)

Release Date

2021-09-08

Peptides

Arginine/agmatine antiporter: 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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Arginine/agmatine antiporter

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