SMTL ID : 5d59.1

In meso 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: 9 residues within 4Å: Chain A: Y.30, I.155, N.156, A.159, E.299, N.328, I.332, E.400 Ligands: PHE.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.159 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.427, F.428 Ligands: ALA.1 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.68 Hydrogen bonds: A:Y.30, A:Y.30, A:Y.30, F.2 Salt bridges: A:R.26, A:K.126 pi-Stacking: A:F.428

21 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, A.248, N.251, L.252, I.255 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.234, A:N.251, A:L.252, A:I.255 Hydrogen bonds: A:N.251 78M.4: 4 residues within 4Å: Chain A: A.376, L.377 Ligands: 78M.5, 78M.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.376 78M.5: 10 residues within 4Å: Chain A: L.366, L.369, L.370, I.373, A.376, L.395, V.451 Ligands: 78M.4, 78M.12, 78M.19 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.366, A:L.369, A:L.370, A:I.373, A:A.376, A:L.395 78M.6: 9 residues within 4Å: Chain A: R.80, I.81, I.82, L.212, V.217, L.220, L.221, V.224 Ligands: 78M.23 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.81, A:I.82, A:L.212, A:V.217, A:L.220, A:L.221, A:V.224 Hydrogen bonds: A:L.212, A:L.212 78M.7: 11 residues within 4Å: Chain A: M.96, I.100, A.103, A.173, H.176, V.177, S.180, I.184, F.187 Ligands: 78M.22, PE5.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.100, A:V.177, A:I.184, A:F.187 78M.8: 9 residues within 4Å: Chain A: Y.335, L.370, S.385, L.387, W.388, G.391, A.394, L.395 Ligands: 78M.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.370, A:L.370, A:W.388, A:W.388, A:A.394 Hydrogen bonds: A:S.385 Water bridges: A:S.385 78M.9: 6 residues within 4Å: Chain A: L.294, L.437, L.444, Y.453, F.457 Ligands: 78M.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.294, A:L.437, A:L.444, A:F.457 78M.10: 4 residues within 4Å: Chain A: V.469, F.470, K.473 Ligands: 78M.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.470, A:F.470 Hydrogen bonds: A:K.473, A:K.473 78M.11: 5 residues within 4Å: Chain A: D.315, S.317, W.318, F.319, P.386 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.318, A:F.319 Hydrogen bonds: A:S.317 78M.12: 7 residues within 4Å: Chain A: L.370, Y.378, W.388 Ligands: 78M.4, 78M.5, 78M.8, 78M.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.370, A:W.388, A:W.388 Hydrogen bonds: A:Y.378 78M.13: 9 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, L.97, Y.193, Y.194, L.206 Ligands: 78M.22 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.89, A:L.97, A:Y.194 Hydrogen bonds: A:R.85, A:R.85 78M.14: 12 residues within 4Å: Chain A: I.62, M.66, L.111, F.112, I.115, I.116, I.119, F.231, L.246, L.253 Ligands: 78M.15, 78M.21 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.62, A:F.112, A:I.115, A:I.115, A:I.116, A:I.119, A:F.231, A:F.231, A:L.253 78M.15: 11 residues within 4Å: Chain A: L.69, S.70, T.72, I.73, I.116, I.119, I.120, I.260, Y.264, S.425 Ligands: 78M.14 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.69, A:L.69, A:I.73, A:I.73, A:I.116, A:I.119, A:I.120, A:I.260 78M.17: 8 residues within 4Å: Chain A: F.265, F.289, L.437, Q.440, T.443, L.444 Ligands: 78M.9, 78M.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.265, A:F.289 Hydrogen bonds: A:T.443, A:T.443 78M.18: 1 residues within 4Å: Ligands: 78M.12 No protein-ligand interaction detected (PLIP) 78M.19: 8 residues within 4Å: Chain A: V.451, A.452, S.455, Y.456, L.459, I.466 Ligands: 78M.5, 78M.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.466 Hydrogen bonds: A:S.455 78M.20: 10 residues within 4Å: Chain A: N.251, T.254, I.255, I.258, A.259, V.262, F.263, W.267, Q.440 Ligands: 78M.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.255, A:I.258, A:A.259, A:F.263, A:W.267, A:W.267 Hydrogen bonds: A:N.251 78M.21: 6 residues within 4Å: Chain A: F.112, F.231, I.235, L.246, Y.249 Ligands: 78M.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.112, A:F.231, A:I.235, A:Y.249, A:Y.249 78M.22: 8 residues within 4Å: Chain A: F.89, M.96, F.187, L.190, L.191, Y.194 Ligands: 78M.7, 78M.13 No protein-ligand interaction detected (PLIP) 78M.23: 7 residues within 4Å: Chain A: T.72, I.73, F.76, F.124, L.220, V.224 Ligands: 78M.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.73, A:I.73, A:F.76, A:F.76, A:F.124, A:L.220 Hydrogen bonds: A:T.72 Water bridges: A:S.425 78M.24: 7 residues within 4Å: Chain A: F.9, F.19, S.149, I.150, F.153, L.157, M.333 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.9, A:F.19, A:L.157

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

PO4.16: 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:G.107, A:A.108, A:S.109, A:S.109, A:S.109, A:S.109

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

PE5.25: 4 residues within 4Å: Chain A: G.174, Y.175, H.176 Ligands: 78M.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.175, A:H.176 Water bridges: A:G.174 PE5.26: 7 residues within 4Å: Chain A: Y.38, W.41, F.42, S.45, R.53, Q.170, Y.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.45, A:Q.170 Water bridges: A:E.171, A:E.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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