SMTL ID : 5oxo.1

PepTSt apo structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: S.316, F.319, V.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.316, A:V.321

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

1PE.2: 7 residues within 4Å: Chain A: Y.38, W.41, Q.170, E.171, Y.175, A.311, V.321 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.170, A:Y.175 Water bridges: A:R.53, A:V.321 1PE.3: 7 residues within 4Å: Chain A: Y.30, Y.68, I.155, N.156, W.296, I.332, E.400 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.156, A:S.404

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 7 residues within 4Å: Chain A: Y.39, F.42, A.173, G.174, Y.175, H.176 Ligands: 78N.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.42 Hydrogen bonds: A:Y.175, A:H.176 Water bridges: A:V.177 Salt bridges: A:H.176, A:H.176

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

78N.5: 11 residues within 4Å: Chain A: L.366, L.369, L.370, A.372, I.373, A.376, V.451, S.455 Ligands: 78M.6, 78N.7, 78N.8 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.7: 2 residues within 4Å: Ligands: 78N.5, 78M.6 No protein-ligand interaction detected (PLIP) 78N.8: 8 residues within 4Å: Chain A: F.363, L.370, I.373, Y.378, W.388 Ligands: 78N.5, 78M.9, 78N.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.363, A:F.363, A:L.370 Hydrogen bonds: A:Y.378, A:Y.378 78N.10: 3 residues within 4Å: Ligands: 78N.8, 78M.9, 78N.11 No protein-ligand interaction detected (PLIP) 78N.11: 8 residues within 4Å: Chain A: F.331, Y.335, F.338, L.387, V.390, A.394 Ligands: 78M.9, 78N.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.331, A:Y.335, A:F.338, A:F.338, A:V.390, A:A.394 78N.12: 9 residues within 4Å: Chain A: F.160, F.319, W.323, F.324, 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.324, A:L.327, A:L.327, A:L.330, A:P.386 78N.13: 10 residues within 4Å: Chain A: M.96, A.103, H.176, V.177, S.180, A.183, I.184, F.187 Ligands: CIT.4, 78M.19 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.183, A:I.184, A:F.187, A:F.187 Water bridges: A:H.176 78N.14: 9 residues within 4Å: Chain A: L.49, I.59, F.112, I.115, I.116, I.119, L.246, L.253 Ligands: 78N.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.59, A:F.112, A:I.116, A:I.119 78N.15: 8 residues within 4Å: Chain A: F.112, F.231, N.244, S.245, L.246, Y.249, L.253 Ligands: 78N.14 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.112, A:F.112, A:F.231, A:L.246, A:Y.249, A:Y.249, A:L.253 Hydrogen bonds: A:L.246 78N.16: 8 residues within 4Å: Chain A: M.238, W.243, A.248, N.251, L.252, I.255, A.259, F.263 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.252, A:I.255, A:A.259, A:F.263, A:F.263 Hydrogen bonds: A:S.245, A:N.251 Water bridges: A:G.242 78N.17: 7 residues within 4Å: Chain A: N.251, I.258, L.437, Q.440, T.443, L.444 Ligands: 78M.18 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.258, A:L.437 Hydrogen bonds: A:N.251, A:T.443, A:T.443 Water bridges: A:N.251 78N.20: 11 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, V.93, Y.193, Y.194, K.198, L.201, L.206 Ligands: 78M.19 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, 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 78N.22: 8 residues within 4Å: Chain A: L.212, A.213, P.214, V.217, L.220, L.221, V.224 Ligands: 78N.23 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.212, A:L.220, A:L.221, A:V.224 Hydrogen bonds: A:L.212 Water bridges: A:L.212 78N.23: 5 residues within 4Å: Chain A: V.217, L.221, V.224, S.225 Ligands: 78N.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.217, A:L.221, A:V.224 78N.24: 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, A:F.470 Hydrogen bonds: A:S.472, A:K.473

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

78M.6: 7 residues within 4Å: Chain A: M.362, F.363, L.366, L.369, L.459 Ligands: 78N.5, 78N.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.363, A:L.366, A:L.366, A:L.369, A:L.459 78M.9: 11 residues within 4Å: Chain A: Y.335, L.370, S.385, L.387, W.388, G.391, A.394, L.398 Ligands: 78N.8, 78N.10, 78N.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.335, A:L.370, A:A.394, A:L.398, A:L.398 78M.18: 5 residues within 4Å: Chain A: L.444, A.452, Y.453, Y.456 Ligands: 78N.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.444, A:Y.456 Water bridges: A:L.444, A:S.449 78M.19: 8 residues within 4Å: Chain A: F.89, M.96, F.187, L.191, Y.194, F.195 Ligands: 78N.13, 78N.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.89, A:F.187, A:L.191 Water bridges: A:Y.194 78M.21: 7 residues within 4Å: Chain A: I.82, P.86, W.90, I.116, L.117, I.120, F.124 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.90, A:I.116, 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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