SMTL ID : 5oxp.1

PepTSt in occluded conformation with phosphate ion bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

monomer

Ligands

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: D.48, F.106, G.107, A.108, S.109 Ligands: 78N.14 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.48, 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: I.51, T.52, T.55, P.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.52, A:T.55, A:T.55, A:T.55 PO4.3: 5 residues within 4Å: Chain A: Y.30, Y.68, E.299, E.300 Ligands: 1PE.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.30, A:Y.30, A:S.303 Water bridges: A:R.33, A:Y.68, A:E.299, A:E.300, A:E.300 PO4.4: 5 residues within 4Å: Chain A: F.76, D.79, R.80, D.210 Ligands: 78N.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.79, A:D.210, A:D.210 PO4.5: 4 residues within 4Å: Chain A: P.351, S.352, T.355, K.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.352, A:S.352 Salt bridges: A:K.473

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

1PE.6: 9 residues within 4Å: Chain A: W.343, P.351, S.353, F.357, M.401, L.402, S.404, G.407, L.408 No protein-ligand interaction detected (PLIP) 1PE.7: 14 residues within 4Å: Chain A: E.22, R.26, Y.30, Y.68, S.130, N.156, W.296, I.332, E.400, V.406, W.427, F.428, S.431 Ligands: PO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.26, A:R.26, A:R.26

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

78N.8: 7 residues within 4Å: Chain A: L.366, L.369, A.372, A.376, V.451, S.455 Ligands: 78N.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.372, A:A.376 Hydrogen bonds: A:S.455 78N.9: 5 residues within 4Å: Chain A: L.377, Y.378, W.388 Ligands: 78N.8, 78M.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.378, A:Y.378 78N.11: 10 residues within 4Å: Chain A: F.160, L.164, W.318, W.323, F.324, S.326, S.385, P.386, L.387 Ligands: 78M.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.160, A:L.164, A:F.324, A:L.387 78N.12: 8 residues within 4Å: Chain A: M.96, I.100, A.103, H.176, V.177, S.180, A.183, F.187 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.183, A:F.187 Water bridges: A:V.177 78N.13: 8 residues within 4Å: Chain A: F.106, S.109, A.110, G.113, I.116, L.117, I.120 Ligands: 78N.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.116, A:L.117, A:I.120 78N.14: 12 residues within 4Å: Chain A: D.48, L.49, I.59, I.62, M.66, I.115, I.116, I.119, L.246, L.253 Ligands: PO4.1, 78N.15 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.49, A:I.59, A:I.62, A:I.115, A:I.115, A:I.116, A:I.119, A:L.246, A:L.246, A:L.253 Hydrogen bonds: A:D.48 78N.15: 10 residues within 4Å: Chain A: F.112, I.116, F.231, I.235, N.244, S.245, L.246, Y.249 Ligands: 78N.13, 78N.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.116, A:I.116, A:F.231, A:F.231, A:I.235, A:Y.249 78N.16: 9 residues within 4Å: Chain A: I.234, M.238, W.243, A.248, N.251, L.252, I.255, F.263 Ligands: 78N.23 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.234, A:L.252, A:I.255, A:F.263 Hydrogen bonds: A:N.251 78N.17: 9 residues within 4Å: Chain A: S.58, P.247, N.251, I.258, L.437, Q.440, L.441, T.443 Ligands: 78M.18 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.258, A:I.258, A:L.437, A:L.441 Hydrogen bonds: A:S.58, A:S.58, A:N.251, A:T.443 78N.19: 9 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, V.93, Y.193, Y.194, K.198, L.206 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: 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, A:K.198, A:K.198 78N.20: 5 residues within 4Å: Chain A: R.80, L.212, L.220, V.224 Ligands: 78N.21 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.212, A:L.220, A:V.224 Hydrogen bonds: A:L.212, A:L.212 78N.21: 3 residues within 4Å: Chain A: V.217, L.221 Ligands: 78N.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.217, A:L.221 78N.22: 6 residues within 4Å: Chain A: T.72, F.76, V.224, A.227 Ligands: PO4.4, 78N.23 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.76, A:F.76, A:V.224, A:A.227 Hydrogen bonds: A:S.421, A:S.421 Water bridges: A:F.76 78N.23: 11 residues within 4Å: Chain A: T.72, I.73, F.231, V.256, I.260, Y.264, Q.422, S.425, L.429 Ligands: 78N.16, 78N.22 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.73, A:F.231, A:F.231, A:V.256, A:I.260 Hydrogen bonds: A:Q.422, A:S.425

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

78M.10: 11 residues within 4Å: Chain A: Y.335, L.370, Y.378, S.385, L.387, W.388, G.391, A.394, L.395 Ligands: 78N.9, 78N.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.387, A:W.388, A:A.394, A:L.395 78M.18: 8 residues within 4Å: Chain A: L.437, L.444, S.449, A.452, Y.453, Y.456, F.457 Ligands: 78N.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.437, A:L.444

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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