SMTL ID : 5oxq.1

PepTSt in complex with HEPES (300 mM)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: S.316, S.317, F.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.319, A:F.319, A:V.321

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: D.48, F.106, G.107, A.108, S.109 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.107, A:A.108, A:S.109, A:S.109, A:S.109, A:S.109 PO4.3: 5 residues within 4Å: Chain A: F.42, G.174, Y.175, H.176 Ligands: 78N.16 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.175, A:H.176 Water bridges: A:A.173, A:G.174 Salt bridges: A:H.176 PO4.4: 6 residues within 4Å: Chain A: H.50, I.51, T.52, T.55, L.246, P.247 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.50, A:T.52, A:T.55, A:T.55, A:T.55 PO4.5: 5 residues within 4Å: Chain A: R.26, Y.30, K.126, I.155 Ligands: EPE.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.30, A:Y.30 Salt bridges: A:R.26, A:K.126

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 4 residues within 4Å: Chain A: Y.38, Q.170, Y.175, A.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.170

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 13 residues within 4Å: Chain A: Y.30, Y.68, W.296, E.299, E.300, G.302, S.303, Q.325, N.328, I.332, E.400, S.404 Ligands: PO4.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.300, A:G.302, A:S.303, A:S.303, A:S.404 Salt bridges: A:E.299, A:E.299, A:E.300, A:E.400, A:E.400 EPE.8: 7 residues within 4Å: Chain A: Y.378, K.383, V.384, S.385, W.388 Ligands: 78N.11, 78M.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.385

14 x 78N: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE(Non-covalent)(Non-functional Binders)

78N.9: 9 residues within 4Å: Chain A: L.366, L.369, L.370, I.373, A.376, V.451, S.455 Ligands: 78M.10, 78N.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.370, A:I.373, A:I.373, A:A.376 Hydrogen bonds: A:S.455 78N.11: 10 residues within 4Å: Chain A: F.363, L.370, I.373, Y.378, W.388, L.398 Ligands: EPE.8, 78N.9, 78M.12, 78N.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.363, A:L.370, A:I.373, A:L.398 Hydrogen bonds: A:Y.378, A:Y.378 78N.13: 3 residues within 4Å: Ligands: 78N.11, 78M.12, 78N.14 No protein-ligand interaction detected (PLIP) 78N.14: 5 residues within 4Å: Chain A: F.331, L.387, V.390 Ligands: 78M.12, 78N.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.331, A:V.390 78N.15: 8 residues within 4Å: Chain A: F.160, W.318, F.319, W.323, S.326, L.330, P.386, L.387 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.160, A:F.319, A:L.330, A:P.386 78N.16: 10 residues within 4Å: Chain A: M.96, A.103, A.173, H.176, V.177, S.180, A.183, I.184 Ligands: PO4.3, 78M.23 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.177, A:A.183, A:I.184 Water bridges: A:H.176 78N.17: 6 residues within 4Å: Chain A: F.106, S.109, G.113, I.116, L.117, I.120 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.116, A:L.117 Hydrogen bonds: A:S.109 78N.18: 12 residues within 4Å: Chain A: L.49, I.59, I.62, M.66, I.73, F.112, I.115, I.116, I.119, L.246, L.253 Ligands: 78N.19 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.59, A:I.62, A:I.73, A:F.112, A:I.115, A:I.116, A:I.119, A:L.246, A:L.253 78N.19: 6 residues within 4Å: Chain A: F.112, F.231, N.244, L.246, Y.249 Ligands: 78N.18 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.112, A:F.112, A:F.231, A:F.231, A:L.246, A:Y.249 Hydrogen bonds: A:L.246 78N.20: 8 residues within 4Å: Chain A: I.234, G.242, W.243, N.244, S.245, A.248, N.251, I.255 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.234, A:W.243, A:W.243, A:A.248, A:I.255 Hydrogen bonds: A:N.244, A:S.245, A:S.245, A:S.245, A:N.251 78N.21: 7 residues within 4Å: Chain A: N.251, I.258, L.437, Q.440, T.443, L.444 Ligands: 78M.22 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.258, A:L.437, A:Q.440 Hydrogen bonds: A:N.251, A:N.251, A:T.443 78N.24: 11 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, V.93, Y.193, G.197, K.198, L.201, L.206 Ligands: 78M.23 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:F.89, A:W.90, A:V.93 Hydrogen bonds: A:R.85 78N.25: 7 residues within 4Å: Chain A: I.81, L.212, A.213, P.214, L.220, L.221 Ligands: 78N.26 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.81, A:L.212, A:L.220, A:L.221 Hydrogen bonds: A:L.212 Water bridges: A:L.212 78N.26: 5 residues within 4Å: Chain A: V.217, L.221, S.225, V.228 Ligands: 78N.25 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.217, A:L.221, A:V.228

4 x 78M: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE(Non-covalent)

78M.10: 5 residues within 4Å: Chain A: M.362, L.369, L.459, V.462 Ligands: 78N.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.369, A:L.459, A:V.462 78M.12: 10 residues within 4Å: Chain A: Y.335, L.370, S.385, L.387, W.388, L.398 Ligands: EPE.8, 78N.11, 78N.13, 78N.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.370, A:W.388, A:L.398 78M.22: 7 residues within 4Å: Chain A: F.265, F.289, I.290, V.293, L.294, L.437 Ligands: 78N.21 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.265, A:F.265, A:F.289, A:I.290, A:V.293, A:L.294, A:L.437 78M.23: 8 residues within 4Å: Chain A: M.96, F.187, L.190, L.191, Y.194, F.195 Ligands: 78N.16, 78N.24 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.187, A:L.190, A:L.190 Hydrogen bonds: A:Y.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez Molledo, M. et al., Multispecific Substrate Recognition in a Proton-Dependent Oligopeptide Transporter. Structure (2018)

Release Date

2018-02-21

Peptides

Di-or tripeptide:H+ symporter: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Di-or tripeptide:H+ symporter

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