SMTL ID : 6fmy.1

IMISX-EP of S-PepTSt

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

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

78M.1: 6 residues within 4Å: Chain A: M.238, W.243, S.245, A.248, N.251, I.255 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.248, A:N.251, A:I.255 Hydrogen bonds: A:S.245 78M.2: 3 residues within 4Å: Chain A: A.376 Ligands: 78M.3, 78M.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.376 Water bridges: A:A.376 78M.3: 9 residues within 4Å: Chain A: L.369, L.370, A.372, I.373, A.376, V.451, S.455 Ligands: 78M.2, 78M.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.369, A:A.372, A:I.373, A:I.373, A:A.376, A:V.451 78M.4: 5 residues within 4Å: Chain A: I.81, L.212, V.217, L.220, L.221 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.81, A:L.212, A:V.217, A:L.220, A:L.221 Hydrogen bonds: A:L.212, A:L.212 78M.5: 7 residues within 4Å: Chain A: M.96, I.100, A.103, H.176, V.177, S.180, I.184 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.100, A:V.177, A:I.184 78M.6: 8 residues within 4Å: Chain A: L.370, Y.378, K.383, V.384, S.385, W.388 Ligands: 78M.9, 78M.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.370, A:W.388, A:W.388 Hydrogen bonds: A:S.385 78M.7: 9 residues within 4Å: Chain A: I.290, L.294, L.437, Q.440, L.441, T.443, L.444, Y.456, F.457 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.290, A:L.294, A:L.437, A:F.457 78M.8: 4 residues within 4Å: Chain A: V.469, F.470, S.472, K.473 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.470 Hydrogen bonds: A:S.472 78M.9: 8 residues within 4Å: Chain A: D.315, W.318, F.319, W.323, S.385, P.386, V.390 Ligands: 78M.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.318, A:F.319, A:P.386, A:V.390 78M.10: 6 residues within 4Å: Chain A: Y.378, W.388 Ligands: 78M.2, 78M.3, 78M.6, 78M.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.388 78M.11: 8 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, Y.193, Y.194, K.198 Ligands: 78M.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:W.90 Hydrogen bonds: A:R.85 78M.12: 1 residues within 4Å: Ligands: 78M.10 No protein-ligand interaction detected (PLIP) 78M.13: 7 residues within 4Å: Chain A: F.112, F.231, I.235, N.244, L.246, Y.249 Ligands: 78M.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.231, A:I.235, A:Y.249 Water bridges: A:N.244 78M.14: 7 residues within 4Å: Chain A: M.96, F.187, L.190, L.191, Y.194, F.195 Ligands: 78M.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.190 78M.15: 7 residues within 4Å: Chain A: S.70, T.72, I.73, F.76, V.77, V.224 Ligands: 78M.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.76, A:V.77, A:V.224 Hydrogen bonds: A:T.72 78M.16: 12 residues within 4Å: Chain A: I.59, I.62, M.66, F.112, I.115, I.116, I.119, F.231, L.246, L.253 Ligands: 78M.13, 78M.15 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.59, A:I.62, A:F.112, A:I.115, A:I.116, A:I.119, A:F.231, A:L.253, A:L.253

1 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.17: 3 residues within 4Å: Chain A: Y.38, Q.170, Y.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.170

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

PO4.18: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C.Y. et al., In situ serial crystallography for rapid de novo membrane protein structure determination. Commun Biol (2018)

Release Date

2018-09-05

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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