SMTL ID : 5d58.1

In meso in situ serial X-ray crystallography structure of the PepTSt-Ala-Phe complex at 100 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ALA: ALANINE(Non-covalent)

ALA.1: 7 residues within 4Å: Chain A: Y.30, N.156, E.299, N.328, I.332, E.400 Ligands: PHE.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.156, A:E.400

1 x PHE: PHENYLALANINE(Non-covalent)

PHE.2: 8 residues within 4Å: Chain A: R.26, Y.30, Y.68, K.126, I.155, W.296, W.427 Ligands: ALA.1 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: F.2, A:Y.30, A:Y.30, A:Y.30 Hydrophobic interactions: A:Y.68 Salt bridges: A:R.26, A:K.126 pi-Stacking: A:W.296, A:F.428

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

PO4.3: 4 residues within 4Å: Chain A: D.48, G.107, A.108, S.109 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.48, A:G.107, A:A.108, A:S.109, A:S.109, A:S.109

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

78M.4: 8 residues within 4Å: Chain A: I.234, M.238, W.243, S.245, A.248, N.251, L.252, I.255 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.234, A:I.255 Hydrogen bonds: A:N.251 Water bridges: A:G.242, A:N.244, A:S.245 78M.5: 5 residues within 4Å: Chain A: I.373, A.376, L.377 Ligands: 78M.6, 78M.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.373, A:I.373, A:A.376 78M.6: 10 residues within 4Å: Chain A: L.369, L.370, A.372, I.373, A.376, L.395, V.451 Ligands: 78M.5, 78M.13, 78M.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.369, A:A.372, A:I.373, A:L.395 78M.7: 4 residues within 4Å: Chain A: L.212, L.220, V.224 Ligands: 78M.20 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 78M.8: 9 residues within 4Å: Chain A: M.96, I.100, H.176, V.177, S.180, A.183, F.187 Ligands: 78M.19, PE5.25 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.100, A:A.183, A:F.187 78M.9: 10 residues within 4Å: Chain A: Y.335, L.370, S.385, L.387, W.388, G.391, A.394, L.395 Ligands: 78M.13, 78M.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.370, A:L.370, A:W.388, A:W.388, A:A.394, A:L.395 Hydrogen bonds: A:S.385 Water bridges: A:S.385 78M.10: 8 residues within 4Å: Chain A: L.294, L.437, L.444, A.452, Y.453, Y.456, F.457 Ligands: 78M.21 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.294, A:L.437, A:F.457, A:F.457 Hydrogen bonds: A:A.452 78M.11: 5 residues within 4Å: Chain A: V.469, F.470, S.472, K.473 Ligands: 78M.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.470, A:F.470 Hydrogen bonds: A:K.473 78M.12: 4 residues within 4Å: Chain A: W.318, F.319, W.323, P.386 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.386 78M.13: 8 residues within 4Å: Chain A: L.370, Y.378, W.388, L.398 Ligands: 78M.5, 78M.6, 78M.9, 78M.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.370, A:W.388, A:L.398 Hydrogen bonds: A:Y.378 78M.14: 9 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, L.97, Y.193, Y.194, K.198 Ligands: 78M.19 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:F.89, A:W.90, A:W.90, A:L.97 Hydrogen bonds: A:R.85, A:K.198, A:K.198 78M.15: 9 residues within 4Å: Chain A: L.69, S.70, T.72, I.73, I.119, S.425, M.426 Ligands: 78M.20, 78M.23 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.69, A:I.73, A:I.119 78M.16: 2 residues within 4Å: Ligands: 78M.9, 78M.13 No protein-ligand interaction detected (PLIP) 78M.17: 8 residues within 4Å: Chain A: L.369, V.451, A.452, S.455, Y.456, L.459 Ligands: 78M.6, 78M.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.369, A:L.459 Hydrogen bonds: A:S.455 78M.18: 7 residues within 4Å: Chain A: F.231, I.232, I.235, N.244, L.246, Y.249 Ligands: 78M.23 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.231, A:I.232, A:I.235, A:Y.249 Hydrogen bonds: A:N.244 78M.19: 8 residues within 4Å: Chain A: M.96, F.187, L.190, L.191, Y.194, F.195 Ligands: 78M.8, 78M.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.190 78M.20: 9 residues within 4Å: Chain A: I.73, F.76, V.77, F.124, L.220, K.223, V.224 Ligands: 78M.7, 78M.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.73, A:I.73, A:F.76, A:F.76, A:F.124 Salt bridges: A:K.223 78M.21: 8 residues within 4Å: Chain A: I.258, V.262, L.437, Q.440, T.443, L.444 Ligands: 78M.10, 78M.24 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.258, A:V.262 Hydrogen bonds: A:T.443, A:T.443 78M.22: 8 residues within 4Å: Chain A: F.9, A.146, S.149, I.150, F.153, L.157, M.333, T.336 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.9, A:F.9, A:F.153, A:L.157, A:L.157 Hydrogen bonds: A:A.146 78M.23: 13 residues within 4Å: Chain A: L.49, I.59, I.62, M.66, L.111, I.115, I.116, I.119, F.231, L.246, L.253 Ligands: 78M.15, 78M.18 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.62, A:I.115, A:I.115, A:I.116, A:I.119, A:F.231, A:L.253, A:L.253 78M.24: 10 residues within 4Å: Chain A: N.251, T.254, I.255, I.258, V.262, F.263, A.266, W.267, Q.440 Ligands: 78M.21 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.255, A:I.258, A:I.258, A:A.266, A:W.267 Hydrogen bonds: A:N.251

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

PE5.25: 6 residues within 4Å: Chain A: Q.170, G.174, Y.175, H.176 Ligands: 78M.8, PE5.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.175, A:H.176 PE5.26: 6 residues within 4Å: Chain A: Y.38, W.41, F.42, Q.170, Y.175 Ligands: PE5.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.170

Links

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Citation

Huang, C.Y. et al., In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-01-13

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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