SMTL ID : 5oxl.1

PepTSt in complex with dipeptide Ala-Leu

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.66 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.48, A:D.48, A:G.107, A:A.108, A:S.109, A:S.109 PO4.2: 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 EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 6 residues within 4Å: Chain A: Y.378, K.383, V.384, S.385, W.388 Ligands: 78M.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.378, A:S.385 pi-Cation interactions: A:Y.378

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

1PE.4: 8 residues within 4Å: Chain A: Y.38, W.41, F.42, Q.170, E.171, Y.175, A.311, V.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.38, A:Q.170 1PE.5: 10 residues within 4Å: Chain A: W.343, P.351, S.352, S.353, K.356, F.357, L.402, I.403, S.404, L.408 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.353, A:S.353, A:K.356

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

78N.6: 6 residues within 4Å: Chain A: L.369, L.370, A.372, A.376, L.395, V.451 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.369, A:A.372, A:A.376, A:L.395 78N.7: 4 residues within 4Å: Chain A: L.370, Y.378, W.388 Ligands: 78M.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.370 Hydrogen bonds: A:Y.378 78N.9: 10 residues within 4Å: Chain A: F.160, L.164, W.318, F.319, W.323, S.326, L.330, S.385, P.386, L.387 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.160, A:L.164, A:F.319, A:W.323, A:L.330, A:L.330 78N.10: 8 residues within 4Å: Chain A: M.96, I.100, A.103, H.176, V.177, S.180, A.183, I.184 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.100, A:A.183, A:I.184 78N.11: 8 residues within 4Å: Chain A: M.238, W.243, S.245, A.248, N.251, L.252, I.255, F.263 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.243, A:A.248, A:L.252, A:I.255, A:F.263 Hydrogen bonds: A:S.245, A:N.251 78N.12: 9 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, Y.193, Y.194, G.197, K.198, L.206 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:F.89, A:W.90 Hydrogen bonds: A:R.85, A:G.197 78N.13: 9 residues within 4Å: Chain A: I.73, F.76, I.81, L.212, A.213, P.214, V.217, V.224 Ligands: 78N.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.73, A:F.76, A:I.81, A:L.212, A:V.224 Hydrogen bonds: A:L.212 78N.14: 2 residues within 4Å: Chain A: L.221 Ligands: 78N.13 No protein-ligand interaction detected (PLIP) 78N.15: 11 residues within 4Å: Chain A: F.9, F.19, M.23, S.149, I.150, F.153, L.157, T.336, A.340, G.407, L.408 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.9, A:F.19, A:I.150, A:F.153, A:F.153, A:L.157 Hydrogen bonds: A:S.149, A:S.149, A:G.407, A:L.408

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

78M.8: 10 residues within 4Å: Chain A: F.331, Y.335, L.370, S.385, L.387, W.388, G.391, L.395 Ligands: EPE.3, 78N.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.331, A:L.370, A:L.395

1 x ALA: ALANINE(Non-covalent)

ALA.16: 8 residues within 4Å: Chain A: Y.30, N.156, A.159, E.299, N.328, I.332, E.400 Ligands: LEU.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.30, A:A.159 Hydrogen bonds: A:N.156, A:N.328, A:N.328

1 x LEU: LEUCINE(Non-covalent)

LEU.17: 9 residues within 4Å: Chain A: R.26, Y.30, Y.68, K.126, I.155, W.296, W.427, S.431 Ligands: ALA.16 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.296, A:W.296, A:W.296, A:W.427 Hydrogen bonds: A:Y.30, A:Y.30, A:Y.30, A:Y.68, L.17 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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