SMTL ID : 6yog.1

Structure of PepTSt from COC IMISX setup collected by still serial crystallography on crystals prelocated by 2D X-ray phase-contrast imaging

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: D.48, G.107, A.108, S.109 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.107, A:A.108, A:S.109, A:S.109, A:S.109, A:S.109 Water bridges: A:F.106

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

78M.2: 6 residues within 4Å: Chain A: I.234, M.238, W.243, A.248, N.251, L.252 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.234, A:N.251, A:L.252 Hydrogen bonds: A:N.251 78M.3: 3 residues within 4Å: Chain A: I.373, A.376 Ligands: 78M.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.373 78M.4: 10 residues within 4Å: Chain A: L.366, L.369, L.370, A.372, I.373, A.376, V.451 Ligands: 78M.3, 78M.11, 78M.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.366, A:L.369, A:L.370, A:A.372, A:I.373, A:I.373, A:A.376 Hydrogen bonds: A:A.376 78M.5: 6 residues within 4Å: Chain A: L.212, P.214, V.217, L.220, L.221 Ligands: 78M.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.220, A:L.221 Hydrogen bonds: A:L.212 Water bridges: A:L.212 78M.6: 8 residues within 4Å: Chain A: M.96, I.100, H.176, V.177, S.180, F.187 Ligands: 78M.17, PG0.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.100, A:F.187, A:F.187 78M.7: 9 residues within 4Å: Chain A: D.315, L.370, S.385, L.387, W.388, G.391, A.394 Ligands: 78M.10, 78M.11 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 Hydrogen bonds: A:D.315 Water bridges: A:K.383, A:S.385 78M.8: 9 residues within 4Å: Chain A: I.290, L.294, L.437, L.441, S.449, A.452, Y.453, F.457 Ligands: 78M.19 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.290, A:L.294, A:L.437, A:L.437, A:L.441 Hydrogen bonds: A:S.449, A:A.452 78M.9: 3 residues within 4Å: Chain A: V.469, F.470 Ligands: 78M.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.469, A:F.470 Hydrogen bonds: A:V.469 78M.10: 5 residues within 4Å: Chain A: W.318, F.319, W.323, P.386 Ligands: 78M.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.318, A:W.318, A:F.319, A:F.319 Hydrogen bonds: A:S.317 78M.11: 7 residues within 4Å: Chain A: L.370, Y.378, W.388, L.398 Ligands: 78M.4, 78M.7, 78M.14 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.12: 9 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, Y.193, Y.194, K.198, L.206 Ligands: 78M.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:F.89, A:W.90, A:W.90, A:W.90 Hydrogen bonds: A:R.85 78M.13: 13 residues within 4Å: Chain A: L.69, T.72, I.73, I.116, I.119, I.260, Y.264, M.423, S.425, M.426, L.429 Ligands: 78M.16, 78M.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.69, A:L.69, A:I.73, A:I.73, A:I.116, A:I.119 78M.14: 1 residues within 4Å: Ligands: 78M.11 No protein-ligand interaction detected (PLIP) 78M.15: 7 residues within 4Å: Chain A: L.369, S.455, Y.456, L.459, V.462 Ligands: 78M.4, 78M.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.369, A:V.462 Hydrogen bonds: A:S.455 78M.16: 8 residues within 4Å: Chain A: F.112, F.231, I.235, N.244, L.246, Y.249 Ligands: 78M.13, 78M.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.112, A:F.231, A:F.231, A:I.235, A:Y.249 Hydrogen bonds: A:N.244 78M.17: 7 residues within 4Å: Chain A: F.89, F.187, L.190, L.191, Y.194 Ligands: 78M.6, 78M.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.190 78M.18: 5 residues within 4Å: Chain A: T.72, I.73, F.76, F.124 Ligands: 78M.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.73, A:I.73, A:F.76, A:F.76, A:F.124 Hydrogen bonds: A:T.72 Water bridges: A:F.76 78M.19: 6 residues within 4Å: Chain A: L.437, Q.440, T.443, L.444 Ligands: 78M.8, 78M.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.440 Hydrogen bonds: A:T.443, A:T.443 78M.20: 13 residues within 4Å: Chain A: L.49, I.59, I.62, M.66, L.111, F.112, I.115, I.116, F.231, L.246, L.253 Ligands: 78M.13, 78M.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.62, A:F.112, A:I.115, A:I.115, A:I.116, A:F.231 78M.21: 11 residues within 4Å: Chain A: N.251, T.254, 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:I.258, A:A.259, A:F.263, A:A.266, A:W.267 Hydrogen bonds: A:N.251

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

PG0.22: 5 residues within 4Å: Chain A: G.174, Y.175, H.176 Ligands: 78M.6, PGE.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.175, A:H.176

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

PGE.23: 6 residues within 4Å: Chain A: Y.38, W.41, F.42, Q.170, Y.175 Ligands: PG0.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martiel, I. et al., Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography. Iucrj (2020)

Release Date

2020-11-04

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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