SMTL ID : 5oxn.1

PepTSt in complex with dipeptide Phe-Ala

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: D.48, F.106, G.107, A.108, S.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.107, A:A.108, A:S.109, A:S.109 PO4.2: 5 residues within 4Å: Chain A: H.50, I.51, T.52, T.55, P.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.50, A:T.52, A:T.55

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

NA.3: 2 residues within 4Å: Chain A: S.316, F.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.316, A:V.321

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

78N.4: 9 residues within 4Å: Chain A: L.366, L.369, L.370, A.372, I.373, A.376, V.451, S.455 Ligands: 78N.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.370, A:A.372, A:I.373, A:I.373, A:A.376 Hydrogen bonds: A:S.455 Water bridges: A:G.375 78N.5: 5 residues within 4Å: Chain A: L.370, Y.378, W.388 Ligands: 78N.4, 78M.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.370, A:W.388 Hydrogen bonds: A:Y.378, A:Y.378 78N.7: 11 residues within 4Å: Chain A: F.160, W.318, F.319, W.323, F.324, S.326, L.327, 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:L.327, A:L.330, A:P.386 78N.8: 6 residues within 4Å: Chain A: I.100, A.103, H.176, V.177, S.180, I.184 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.100, A:V.177, A:I.184 Water bridges: A:H.176 78N.9: 14 residues within 4Å: Chain A: L.49, I.59, I.62, M.66, S.70, I.73, A.108, F.112, I.115, I.116, I.119, L.246, L.253 Ligands: 78N.10 7 PLIP interactions: 7 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:L.253 78N.10: 7 residues within 4Å: Chain A: F.112, I.116, N.244, S.245, L.246, Y.249 Ligands: 78N.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.112, A:F.112, A:I.116 Hydrogen bonds: A:N.244 78N.11: 11 residues within 4Å: Chain A: I.234, M.238, W.243, S.245, A.248, N.251, L.252, I.255, A.259, I.260, F.263 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.234, A:I.255, A:I.255, A:A.259, A:I.260, A:F.263, A:F.263 Hydrogen bonds: A:S.245, A:N.251 78N.12: 11 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, V.93, Y.193, Y.194, G.197, K.198, L.201, L.206 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:F.89, A:W.90, A:W.90, A:V.93, A:Y.194 Hydrogen bonds: A:R.85 78N.13: 9 residues within 4Å: Chain A: I.73, V.77, I.81, L.212, A.213, P.214, V.217, L.220 Ligands: 78N.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.73, A:V.77, A:V.217, A:L.220 Hydrogen bonds: A:L.212 Water bridges: A:L.212 78N.14: 4 residues within 4Å: Chain A: V.217, L.221, S.225 Ligands: 78N.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.217 78N.15: 5 residues within 4Å: Chain A: I.466, V.469, F.470, S.472, K.473 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.466, A:F.470, A:F.470 Hydrogen bonds: A:S.472, A:K.473 Water bridges: A:R.474

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

78M.6: 10 residues within 4Å: Chain A: Y.335, F.338, L.370, S.385, L.387, W.388, G.391, A.394, L.398 Ligands: 78N.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.338, A:L.370, A:A.394, A:L.398 Hydrogen bonds: A:S.385

1 x PHE: PHENYLALANINE(Non-covalent)

PHE.16: 9 residues within 4Å: Chain A: Y.30, A.159, E.299, Q.325, N.328, P.329, I.332, E.400 Ligands: ALA.17 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:A.159, A:N.328 Hydrogen bonds: A:N.328, A:E.400 pi-Stacking: A:Y.30

1 x ALA: ALANINE(Non-covalent)

ALA.17: 5 residues within 4Å: Chain A: Y.30, Y.68, W.296, S.431 Ligands: PHE.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.68, A:W.296 Hydrogen bonds: A:Y.30, A:Y.68, A:Y.68, A:Y.68 Water bridges: A:R.26 Salt bridges: A:K.126

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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