SMTL ID : 7cqm.1 (1 other biounit)

PlsY grown in LCP soaked with selenourea for 22 min

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

8 x SEY: selenourea(Non-covalent)

SEY.1: 3 residues within 4Å: Chain A: R.137, T.195 Ligands: SEY.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.195, A:T.195, A:T.195 Water bridges: A:R.137, A:R.137 SEY.2: 2 residues within 4Å: Chain A: F.75, S.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.79 SEY.3: 4 residues within 4Å: Chain A: T.18, E.21, V.22, F.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.18, A:T.18 SEY.4: 5 residues within 4Å: Chain A: V.139, H.191, R.192, F.193 Ligands: 79M.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.191, A:R.192 SEY.5: 3 residues within 4Å: Chain A: G.194, T.195 Ligands: SEY.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.195 Water bridges: A:T.195 SEY.6: 4 residues within 4Å: Chain A: R.32, N.33, V.34, G.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.35, A:G.35 Water bridges: A:N.33 SEY.7: 4 residues within 4Å: Chain A: Y.95, P.96, F.98, F.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.96, A:F.101 SEY.23: 4 residues within 4Å: Chain A: F.155, G.158, Y.159, L.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.155, A:G.158

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 7 residues within 4Å: Chain A: S.36, N.38, T.42, N.43, R.46, G.104, K.105 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.36, A:N.38, A:N.43, A:K.105 Water bridges: A:T.42, A:T.42, A:K.105, A:K.105, A:K.105 Salt bridges: A:R.46, A:K.105 SO4.9: 10 residues within 4Å: Chain A: G.40, A.41, D.60, H.93, G.104, K.105, G.106, V.107, A.108, T.109 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.41, A:D.60, A:D.60, A:G.106, A:A.108, A:T.109 Water bridges: A:T.42, A:T.42, A:K.105, A:K.105, A:V.107 Salt bridges: A:H.93 SO4.10: 3 residues within 4Å: Chain A: K.102, R.177, R.179 8 PLIP interactions: 8 interactions with chain A Water bridges: A:N.38, A:K.102, A:K.102, A:R.177, A:R.177 Salt bridges: A:K.102, A:R.177, A:R.179 SO4.11: 3 residues within 4Å: Chain A: I.77, Y.159, P.160 No protein-ligand interaction detected (PLIP) SO4.12: 6 residues within 4Å: Chain A: R.46, K.105, N.181, H.191 Ligands: 79M.14, 79M.16 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.181 Water bridges: A:R.46, A:R.184, A:E.190 Salt bridges: A:R.46, A:K.105, A:H.191 SO4.13: 4 residues within 4Å: Chain A: K.25, G.28, V.29, D.30 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.25 Salt bridges: A:K.25

10 x 79M: (2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate(Non-covalent)

79M.14: 21 residues within 4Å: Chain A: T.42, F.57, K.105, V.107, A.110, L.111, V.114, S.125, F.126, W.129, V.139, S.143, A.146, T.147, A.150, A.167, I.170, G.171, H.178 Ligands: SO4.12, 79M.16 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.57, A:V.107, A:A.110, A:L.111, A:V.114, A:W.129, A:W.129, A:W.129, A:A.150, A:I.170 Hydrogen bonds: A:K.105, A:S.143, A:S.143 79M.15: 5 residues within 4Å: Chain A: I.168, A.172, L.173, Y.176 Ligands: 79M.20 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.168, A:A.172, A:A.172, A:Y.176 Hydrogen bonds: A:Y.176 79M.16: 15 residues within 4Å: Chain A: A.41, T.42, T.45, R.46, V.54, F.57, L.111, F.115, F.126, V.139, H.191 Ligands: SEY.4, SO4.12, 79M.14, 79M.18 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.41, A:V.54, A:F.57, A:F.57, A:L.111, A:F.115, A:F.126, A:F.126, A:F.126 Water bridges: A:R.46, A:R.46 79M.17: 10 residues within 4Å: Chain A: T.147, I.148, F.151, G.171, A.172, I.175, Y.176, R.179, E.180 Ligands: 79M.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.151, A:A.172, A:Y.176 Hydrogen bonds: A:E.180 79M.18: 12 residues within 4Å: Chain A: F.57, F.58, F.61, F.65, V.72, K.73, I.77, F.115, A.116, V.117, P.119 Ligands: 79M.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.57, A:F.58, A:F.58, A:F.61, A:F.61, A:F.65, A:F.65 Salt bridges: A:K.73 79M.19: 7 residues within 4Å: Chain A: S.118, S.120, F.124, F.153, A.157, Y.159 Ligands: 79M.24 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.153, A:F.153, A:F.153 Hydrogen bonds: A:S.118, A:Y.159 79M.20: 8 residues within 4Å: Chain A: F.151, F.155, V.161, L.164, F.165, I.168 Ligands: 79M.15, 79M.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.151, A:F.155, A:V.161, A:L.164, A:I.168 79M.21: 5 residues within 4Å: Chain A: P.119, S.120, L.123 Ligands: 79M.22, 79M.24 No protein-ligand interaction detected (PLIP) 79M.22: 3 residues within 4Å: Chain A: L.123 Ligands: 79M.21, 79M.24 No protein-ligand interaction detected (PLIP) 79M.24: 5 residues within 4Å: Chain A: S.120, F.124 Ligands: 79M.19, 79M.21, 79M.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, Z.P. et al., Selenourea for experimental phasing of membrane protein crystals grown in lipid cubic phase. Crystals (2022)

Release Date

2021-08-11

Peptides

Glycerol-3-phosphate acyltransferase: 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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Glycerol-3-phosphate acyltransferase

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