SMTL ID : 5oxm.1

PepTSt in complex with dipeptide Asp-Glu

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

4 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 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 PO4.2: 4 residues within 4Å: Chain A: G.174, Y.175, H.176 Ligands: 78N.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.175, A:H.176 Water bridges: A:A.173, A:G.174, A:V.177 Salt bridges: A:H.176 PO4.3: 4 residues within 4Å: Chain A: N.239, N.244, Y.249 Ligands: 78N.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.239, A:N.239, A:N.244 PO4.4: 7 residues within 4Å: Chain A: Y.30, E.299, E.300, G.302, S.303, Q.325 Ligands: ASP.21 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.300, A:S.303, A:S.303 Water bridges: A:R.33, A:E.300, A:E.300, A:G.302, A:S.303

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

78N.5: 8 residues within 4Å: Chain A: L.366, L.369, L.370, A.372, A.376, V.451, S.455 Ligands: 78N.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.369, A:A.372, A:A.376 Hydrogen bonds: A:S.455 78N.6: 6 residues within 4Å: Chain A: L.370, I.373, Y.378, W.388 Ligands: 78N.5, 78M.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.370, A:I.373, A:W.388 Hydrogen bonds: A:Y.378, A:Y.378 78N.8: 6 residues within 4Å: Chain A: F.331, Y.335, L.387, V.390, A.394 Ligands: 78M.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.331, A:Y.335, A:L.387, A:V.390, A:A.394 78N.9: 8 residues within 4Å: Chain A: D.315, W.318, F.319, W.323, F.324, L.327, L.330, P.386 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.318, A:F.319, A:F.319, A:W.323, A:F.324, A:L.327, A:L.330, A:P.386 Hydrogen bonds: A:D.315 78N.10: 10 residues within 4Å: Chain A: M.96, I.100, H.176, V.177, S.180, A.183, I.184, F.187 Ligands: PO4.2, 78M.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.177, A:A.183, A:I.184, A:F.187 78N.11: 8 residues within 4Å: Chain A: F.106, S.109, A.110, G.113, I.116, L.117, I.120 Ligands: 78N.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.116, A:L.117, A:L.117, A:I.120 Hydrogen bonds: A:S.109, A:S.109 78N.12: 13 residues within 4Å: Chain A: L.49, I.59, I.62, M.66, L.69, S.70, F.112, I.115, I.116, I.119, L.246, L.253 Ligands: 78N.13 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.59, A:I.62, A:M.66, A:L.69, A:F.112, A:I.115, A:I.116, A:L.246, A:L.253 78N.13: 8 residues within 4Å: Chain A: F.112, F.231, N.244, L.246, Y.249 Ligands: PO4.3, 78N.12, 78N.20 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.112, A:L.246, A:Y.249, A:Y.249 Hydrogen bonds: A:N.244 78N.14: 3 residues within 4Å: Chain A: V.237, L.240 Ligands: 78N.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.237 78N.15: 8 residues within 4Å: Chain A: G.242, W.243, S.245, A.248, N.251, L.252, I.255 Ligands: 78N.14 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.243, A:W.243, A:A.248, A:I.255 Hydrogen bonds: A:S.245, A:S.245, A:S.245, A:N.251 78N.17: 12 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 Ligands: 78M.16 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:W.90, A:W.90, A:W.90, A:V.93, A:Y.194 Hydrogen bonds: A:R.85, A:Y.193 78N.18: 6 residues within 4Å: Chain A: R.80, I.81, L.212, L.220 Ligands: 78N.19, 78N.20 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.81, A:L.220 Hydrogen bonds: A:L.212 78N.19: 3 residues within 4Å: Chain A: V.217, L.221 Ligands: 78N.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.217, A:L.221 78N.20: 8 residues within 4Å: Chain A: I.73, F.76, V.77, F.124, V.224 Ligands: 78N.11, 78N.13, 78N.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.73, A:F.124, A:V.224

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

78M.7: 10 residues within 4Å: Chain A: Y.335, Y.378, V.384, S.385, L.387, W.388, G.391, L.395 Ligands: 78N.6, 78N.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.387, A:W.388, A:W.388, A:W.388, A:L.395 Hydrogen bonds: A:S.385, A:S.385, A:W.388 78M.16: 9 residues within 4Å: Chain A: F.89, M.96, L.97, F.187, L.190, L.191, Y.194 Ligands: 78N.10, 78N.17 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:L.97, A:F.187, A:L.190, A:L.190, A:L.191, A:Y.194

1 x ASP: ASPARTIC ACID(Non-covalent)

ASP.21: 11 residues within 4Å: Chain A: Y.30, I.155, N.156, E.299, Q.325, N.328, P.329, I.332, E.400 Ligands: PO4.4, GLU.22 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:Y.30, A:N.328, A:E.400, D.21 Water bridges: A:A.159, A:Q.325

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.22: 9 residues within 4Å: Chain A: R.26, Y.30, Y.68, K.126, I.155, W.296, E.300, S.431 Ligands: ASP.21 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:Y.30, A:Y.30, A:E.300, A:S.431, E.22 Salt bridges: A:R.26, 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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