SMTL ID : 6eia.1

PepTSt in complex with HEPES (100 mM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 5 residues within 4Å: Chain A: F.42, G.174, Y.175, H.176 Ligands: 78N.16 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: 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 PO4.4: 5 residues within 4Å: Chain A: R.26, Y.30, K.126, I.155 Ligands: EPE.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.30 Salt bridges: A:R.26, A:K.126

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 5 residues within 4Å: Chain A: Y.38, W.41, Q.170, Y.175, V.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.170, A:Y.175 Water bridges: A:V.321

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

EPE.6: 12 residues within 4Å: Chain A: Y.30, Y.68, W.296, E.299, E.300, G.302, S.303, N.328, I.332, E.400, S.404 Ligands: PO4.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.300, A:G.302, A:S.303, A:S.303, A:S.404 Water bridges: A:R.33, A:Y.68 Salt bridges: A:E.299, A:E.299, A:E.400, A:E.400 EPE.7: 6 residues within 4Å: Chain A: Y.378, V.384, S.385, W.388 Ligands: 78N.11, 78M.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.378, A:S.385 Water bridges: A:D.315, A:K.383

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

78N.8: 10 residues within 4Å: Chain A: L.366, L.369, L.370, I.373, A.376, V.451, S.455 Ligands: 78M.9, 78N.10, 78N.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.366, A:L.369, A:L.370, A:I.373, A:A.376 Hydrogen bonds: A:S.455 78N.10: 2 residues within 4Å: Ligands: 78N.8, 78M.9 No protein-ligand interaction detected (PLIP) 78N.11: 10 residues within 4Å: Chain A: F.363, L.370, I.373, Y.378, W.388, L.398 Ligands: EPE.7, 78N.8, 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: 4 residues within 4Å: Chain A: F.338 Ligands: 78N.11, 78M.12, 78N.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.338 78N.14: 6 residues within 4Å: Chain A: F.331, Y.335, F.338, V.390 Ligands: 78M.12, 78N.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.331, A:Y.335, A:Y.335, A:F.338, A:V.390 78N.15: 9 residues within 4Å: Chain A: F.160, W.318, F.319, W.323, F.324, L.327, L.330, P.386, L.387 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.16: 7 residues within 4Å: Chain A: H.176, V.177, S.180, A.183, F.187 Ligands: PO4.2, 78M.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.183, A:F.187 Water bridges: A:A.173, A:H.176 78N.17: 11 residues within 4Å: Chain A: I.59, I.62, M.66, I.73, F.112, I.115, I.116, I.119, L.246, L.253 Ligands: 78N.18 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.59, A:I.62, A:I.73, A:F.112, A:I.116 78N.18: 8 residues within 4Å: Chain A: F.112, I.116, N.244, S.245, L.246, Y.249 Ligands: 78N.17, 78M.23 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.112, A:F.112, A:I.116, A:L.246, A:Y.249, A:Y.249 78N.19: 9 residues within 4Å: Chain A: I.234, W.243, S.245, A.248, N.251, L.252, I.255, A.259, F.263 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.234, A:W.243, A:L.252, A:I.255, A:I.255, A:F.263 Hydrogen bonds: A:N.251 78N.22: 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.21 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:W.90, A:V.93 Hydrogen bonds: A:R.85 78N.24: 6 residues within 4Å: Chain A: L.212, P.214, V.217, L.220, L.221 Ligands: 78N.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.220, A:L.221 Hydrogen bonds: A:L.212 Water bridges: A:L.212 78N.25: 5 residues within 4Å: Chain A: V.217, L.221, V.224, S.225 Ligands: 78N.24 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.217, A:L.221, A:V.224

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

78M.9: 9 residues within 4Å: Chain A: V.359, M.362, F.363, L.366, L.369, S.455, L.459 Ligands: 78N.8, 78N.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.359, A:F.363, A:L.366, A:L.369, A:L.459 78M.12: 11 residues within 4Å: Chain A: Y.335, S.385, L.387, W.388, G.391, A.394, L.398 Ligands: EPE.7, 78N.11, 78N.13, 78N.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.394, A:L.398 Hydrogen bonds: A:S.385 78M.20: 6 residues within 4Å: Chain A: I.290, L.294, L.444, A.452, Y.456, F.457 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.290, A:L.294, A:Y.456, A:F.457 78M.21: 8 residues within 4Å: Chain A: F.89, M.96, I.100, F.187, L.191, Y.194 Ligands: 78N.16, 78N.22 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.100, A:F.187, A:L.191, A:Y.194 Hydrogen bonds: A:Y.194 78M.23: 9 residues within 4Å: Chain A: I.82, P.86, W.90, L.94, I.116, L.117, I.120, F.124 Ligands: 78N.18 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.90, A:L.94, A:I.116, A:L.117, A:I.120, A:F.124 Hydrogen bonds: A:I.82

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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