SMTL ID : 6ghj.1

PepTSt in complex with tripeptide Phe-Ala-Gln

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

1 x PHE- ALA- GLN: PHE-ALA-GLN(Non-covalent)

PHE-ALA-GLN.1: 14 residues within 4Å: Chain A: R.26, Y.30, Y.68, K.126, I.155, A.159, W.296, E.299, Q.325, N.328, P.329, I.332, E.400, S.431 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.30, A:Y.68, A:A.159, A:W.296, A:N.328 Hydrogen bonds: A:Y.30, A:N.328, A:N.328 Water bridges: A:R.26, A:Y.68, A:E.299 Salt bridges: A:R.26, A:K.126

3 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.107, A:A.108, A:S.109, A:S.109, A:S.109, A:S.109 Water bridges: A:P.105, A:F.106 PO4.3: 4 residues within 4Å: Chain A: G.174, Y.175, H.176 Ligands: 78N.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.175, A:H.176 Water bridges: A:A.173, A:V.177 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

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

1PE.5: 5 residues within 4Å: Chain A: Y.38, Q.170, E.171, Y.175, A.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.170

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

EPE.6: 7 residues within 4Å: Chain A: Y.378, K.383, V.384, S.385, W.388 Ligands: 78N.10, 78M.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.378, A:S.385

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

NA.7: 4 residues within 4Å: Chain A: S.316, F.319, P.320, V.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.316, A:F.319, A:V.321

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

78N.8: 9 residues within 4Å: Chain A: L.369, L.370, A.372, I.373, A.376, V.451, S.455 Ligands: 78M.9, 78N.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.369, A:L.370, A:A.372, A:A.376 Hydrogen bonds: A:S.455 78N.10: 7 residues within 4Å: Chain A: F.363, L.370, Y.378, W.388 Ligands: EPE.6, 78N.8, 78M.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.363, A:L.370 Hydrogen bonds: A:Y.378 78N.12: 10 residues within 4Å: Chain A: F.160, W.318, F.319, W.323, F.324, S.326, L.330, P.386, L.387, V.390 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.160, A:F.319, A:F.319, A:F.324, A:F.324, A:L.330, A:P.386 78N.13: 8 residues within 4Å: Chain A: M.96, I.100, H.176, V.177, S.180, A.183, I.184 Ligands: PO4.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.100, A:I.100, A:A.183, A:I.184 Water bridges: A:H.176 78N.14: 11 residues within 4Å: Chain A: L.49, I.59, I.62, M.66, F.112, I.115, I.116, I.119, L.246, L.253 Ligands: 78N.15 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.59, A:I.62, A:F.112, A:I.115, A:I.116, A:I.119, A:L.246, A:L.253, A:L.253 78N.15: 7 residues within 4Å: Chain A: F.112, F.231, I.232, N.244, L.246, Y.249 Ligands: 78N.14 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.112, A:F.112, A:F.231, A:F.231, A:I.232, A:I.232, A:Y.249, A:Y.249 78N.16: 11 residues within 4Å: Chain A: I.234, M.238, W.243, A.248, N.251, L.252, I.255, V.256, A.259, I.260, F.263 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.234, A:W.243, A:L.252, A:I.255, A:I.255, A:V.256, A:A.259, A:I.260, A:F.263 78N.17: 7 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, Y.193, Y.194, L.206 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.89, A:W.90, A:Y.194 Hydrogen bonds: A:R.85 Water bridges: A:R.85, A:Y.193, A:Y.194, A:Y.194 78N.18: 7 residues within 4Å: Chain A: I.81, L.212, P.214, V.217, L.220, V.224 Ligands: 78N.19 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.81, A:L.212, A:L.220, A:V.224 Hydrogen bonds: A:L.212 Water bridges: A:L.212 78N.19: 3 residues within 4Å: Chain A: L.221, S.225 Ligands: 78N.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.221 78N.20: 4 residues within 4Å: Chain A: V.469, F.470, S.472, K.473 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.470, A:F.470 Hydrogen bonds: A:F.470, A:S.472, A:K.473

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

78M.9: 5 residues within 4Å: Chain A: M.362, L.369, S.455, L.459 Ligands: 78N.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.369, A:L.459 78M.11: 10 residues within 4Å: Chain A: Y.335, L.370, S.385, L.387, W.388, G.391, A.394, L.398 Ligands: EPE.6, 78N.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.370, A:W.388, A:L.398 78M.21: 5 residues within 4Å: Chain A: L.294, L.444, A.452, Y.456, F.457 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.294, A:L.444, A:Y.456, A:F.457

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez Molledo, M. et al., Tripeptide binding in a proton-dependent oligopeptide transporter. FEBS Lett. (2018)

Release Date

2018-09-19

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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