SMTL ID : 7ac6.1

Structure of sponge-phase grown PepTst2 collected by rotation serial crystallography on a COC membrane at a synchrotron source

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x ALA- PHE: Di-or tripeptide:H+ symporter(Non-covalent)

ALA-PHE.1: 13 residues within 4Å: Chain A: R.26, Y.30, Y.68, K.126, I.155, N.156, E.299, N.328, I.332, E.400, W.427, F.428, S.431 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.68 Hydrogen bonds: A:Y.30, A:Y.30, A:N.156, A:E.400 Salt bridges: A:R.26, A:K.126 pi-Stacking: A:F.428

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

PO4.2: 4 residues within 4Å: Chain A: D.48, G.107, A.108, S.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.107, A:A.108, A:S.109, A:S.109

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

78M.3: 7 residues within 4Å: Chain A: I.234, M.238, W.243, S.245, A.248, N.251, L.252 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.234, A:N.251 Hydrogen bonds: A:N.251 78M.4: 2 residues within 4Å: Chain A: A.376 Ligands: 78M.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.376 78M.5: 11 residues within 4Å: Chain A: L.366, L.369, L.370, A.372, I.373, A.376, L.395, V.451 Ligands: 78M.4, 78M.12, 78M.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.366, A:L.369, A:L.369, A:A.372, A:I.373, A:I.373, A:A.376, A:L.395 78M.6: 4 residues within 4Å: Chain A: I.81, L.212, L.220 Ligands: 78M.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.81, A:L.220 Hydrogen bonds: A:L.212 78M.7: 8 residues within 4Å: Chain A: M.96, H.176, V.177, S.180, I.184, F.187 Ligands: 78M.17, PG0.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.184, A:F.187, A:F.187, A:F.187 78M.8: 9 residues within 4Å: Chain A: L.370, S.385, L.387, W.388, G.391, L.395 Ligands: 78M.11, 78M.12, 78M.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.388, A:W.388, A:L.395 Water bridges: A:K.383, A:S.385 78M.9: 6 residues within 4Å: Chain A: L.294, L.444, A.452, Y.453, F.457 Ligands: 78M.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.294 Hydrogen bonds: A:A.452 78M.10: 4 residues within 4Å: Chain A: V.469, F.470, K.473 Ligands: 78M.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.470 78M.11: 8 residues within 4Å: Chain A: D.315, W.318, W.323, F.324, L.327, S.385, P.386 Ligands: 78M.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.324, A:L.327, A:P.386 Hydrogen bonds: A:D.315 78M.12: 7 residues within 4Å: Chain A: L.370, I.373, Y.378, W.388 Ligands: 78M.5, 78M.8, 78M.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.370, A:I.373, A:W.388 Hydrogen bonds: A:Y.378 78M.13: 12 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, V.93, Y.193, Y.194, G.197, K.198, L.201, L.206 Ligands: 78M.17 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:F.89, A:W.90, A:W.90, A:V.93 Hydrogen bonds: A:R.85, A:Y.193 78M.14: 13 residues within 4Å: Chain A: L.69, S.70, T.72, I.73, I.116, I.119, I.260, Y.264, S.425, M.426, L.429 Ligands: 78M.18, 78M.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.69, A:L.69, A:I.73, A:I.116, A:I.119 Hydrogen bonds: A:S.425 78M.15: 2 residues within 4Å: Ligands: 78M.8, 78M.12 No protein-ligand interaction detected (PLIP) 78M.16: 5 residues within 4Å: Chain A: S.455, Y.456, L.459 Ligands: 78M.5, 78M.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.455 78M.17: 9 residues within 4Å: Chain A: M.96, I.100, F.187, L.190, L.191, Y.194, F.195 Ligands: 78M.7, 78M.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.100, A:L.190, A:L.190 78M.18: 7 residues within 4Å: Chain A: T.72, I.73, F.76, V.77, F.124 Ligands: 78M.6, 78M.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.73, A:I.73, A:F.76, A:F.76, A:V.77, A:F.124 78M.19: 7 residues within 4Å: Chain A: V.262, L.437, Q.440, T.443, L.444 Ligands: 78M.9, 78M.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.262, A:Q.440 Hydrogen bonds: A:T.443 78M.20: 10 residues within 4Å: Chain A: I.59, I.62, M.66, L.111, F.112, I.115, I.116, L.246, L.253 Ligands: 78M.14 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.62, A:F.112, A:F.112, A:I.115, A:I.115, A:I.116, A:L.253, A:L.253 78M.21: 10 residues within 4Å: Chain A: N.251, I.255, I.258, A.259, V.262, F.263, A.266, W.267, Q.440 Ligands: 78M.19 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.255, A:I.258, A:A.259, A:V.262, A:A.266, A:W.267, A:W.267 Hydrogen bonds: A:N.251

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.22: 3 residues within 4Å: Chain A: G.174, Y.175 Ligands: 78M.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.175

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.23: 5 residues within 4Å: Chain A: Y.38, Q.170, E.171, Y.175, V.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.170, A:E.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martiel, I. et al., Versatile microporous polymer-based supports for serial macromolecular crystallography. Acta Crystallogr D Struct Biol (2021)

Release Date

2021-09-01

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