SMTL ID : 5oxk.1

PepTSt in complex with dipeptide Ala-Gln

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

3 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.107, A:A.108, A:S.109, 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 PO4.3: 4 residues within 4Å: Chain A: D.79, R.80, D.210, S.421 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.79, A:D.210, A:D.210, A:S.421, A:S.421 Water bridges: A:D.210

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

1PE.4: 6 residues within 4Å: Chain A: Y.38, W.41, F.42, Q.170, Y.175, V.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.170, A:Q.170

12 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, I.373, A.376, V.451, S.455 Ligands: 78N.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.369, A:I.373, A:A.376 Hydrogen bonds: A:S.455 78N.6: 6 residues within 4Å: Chain A: F.363, Y.378, W.388, L.398 Ligands: 78N.5, 78M.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.363, A:F.363, A:W.388, A:L.398 Hydrogen bonds: A:Y.378 78N.8: 4 residues within 4Å: Chain A: F.319, W.323, F.324, L.387 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.319, A:F.324, A:F.324 78N.9: 9 residues within 4Å: Chain A: M.96, I.100, A.103, A.173, H.176, V.177, S.180, A.183, F.187 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.100, A:A.183, A:F.187 78N.10: 9 residues within 4Å: Chain A: V.101, F.106, S.109, A.110, G.113, I.116, L.117, I.120 Ligands: 78N.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.116 Hydrogen bonds: A:S.109 78N.11: 12 residues within 4Å: Chain A: L.49, I.59, M.66, S.70, A.108, L.111, F.112, I.115, I.116, I.119, L.253 Ligands: 78N.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.59, A:I.115, A:I.116 78N.12: 5 residues within 4Å: Chain A: F.112, L.246, Y.249 Ligands: 78N.10, 78N.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.112, A:Y.249 78N.13: 9 residues within 4Å: Chain A: M.238, W.243, S.245, 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:I.255, A:A.259, A:F.263, A:F.263 Hydrogen bonds: A:S.245, A:N.251 78N.14: 7 residues within 4Å: Chain A: N.251, I.255, I.258, V.262, F.263, Q.440 Ligands: 78N.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.255, A:I.258, A:V.262, A:F.263 78N.15: 4 residues within 4Å: Chain A: I.258, L.437, Q.440 Ligands: 78N.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.258, A:L.437 Hydrogen bonds: A:Q.440 78N.16: 9 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, Y.193, Y.194, G.197, K.198, L.206 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:W.90, A:W.90, A:Y.194 Hydrogen bonds: A:R.85, A:Y.193 78N.17: 2 residues within 4Å: Chain A: L.221, V.228 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.221, A:V.228, A:V.228

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

78M.7: 8 residues within 4Å: Chain A: Y.335, L.370, S.385, L.387, W.388, G.391, L.395 Ligands: 78N.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.370, A:L.387, A:L.395 Hydrogen bonds: A:S.385

1 x ALA: ALANINE(Non-covalent)

ALA.18: 6 residues within 4Å: Chain A: N.156, E.299, N.328, I.332, E.400 Ligands: GLN.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.156, A:N.328, A:N.328

1 x GLN: GLUTAMINE(Non-covalent)

GLN.19: 9 residues within 4Å: Chain A: R.26, Y.30, Y.68, K.126, I.155, W.296, W.427, S.431 Ligands: ALA.18 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:Y.30, A:Y.30, A:Y.30, A:S.431, A:S.431, Q.19 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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