SMTL ID : 4c7r.1

Inward facing conformation of the trimeric betaine transporter BetP in complex with lipids

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

4 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 8 residues within 4Å: Chain A: A.119, G.120, M.121, G.122, W.160, W.348, F.351, V.352 No protein-ligand interaction detected (PLIP) FLC.8: 8 residues within 4Å: Chain B: A.118, A.119, G.120, M.121, G.122, W.348, F.351, V.352 No protein-ligand interaction detected (PLIP) FLC.12: 5 residues within 4Å: Chain C: A.119, G.120, M.121, W.348, F.351 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:M.121 Water bridges: C:I.123, C:G.124, C:S.224 FLC.20: 3 residues within 4Å: Chain C: R.138, N.139, E.146 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.138 Salt bridges: C:R.138, C:R.138

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: N.148, G.150 Chain B: S.325, A.326 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: I.96, R.97, I.101, R.181, I.520 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain C: R.97, I.101, D.102, R.181, I.520 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: N.148, G.150 Chain C: S.325, A.326 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: S.325, A.326 Chain C: N.148, G.150 Ligand excluded by PLIP

9 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.3: 10 residues within 4Å: Chain A: F.83, A.90, R.366, L.370 Chain B: S.91, K.92 Ligands: PGT.4, PGT.6, PGT.7, PGT.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.83, A:A.90 Salt bridges: A:R.366 Hydrogen bonds: B:K.92 PGT.4: 16 residues within 4Å: Chain A: F.83, V.86, V.87, S.91, K.92 Chain C: A.90, S.91, K.92, L.162, R.366, L.370, L.374 Ligands: PGT.3, PGT.5, PGT.6, PGT.7 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:F.83, A:F.83, A:F.83, A:F.83, A:V.86, A:V.87, C:L.162, C:L.374 Hydrogen bonds: A:K.92, C:S.91, C:K.92, C:R.366, C:R.366 Salt bridges: C:R.366, C:R.366 PGT.5: 12 residues within 4Å: Chain A: F.83, V.87, Y.521, R.525, R.529 Chain C: R.97, S.364, R.366, E.367, L.370, V.375 Ligands: PGT.4 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.83, A:V.87, C:R.366, C:L.370, C:V.375 Hydrogen bonds: A:Q.528, A:R.529, C:S.364 Salt bridges: A:R.525, C:R.97, C:R.366 PGT.6: 9 residues within 4Å: Chain A: L.312, F.315, F.316 Chain B: F.316 Chain C: L.162, L.312, F.315 Ligands: PGT.3, PGT.4 6 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:L.162, C:L.312, C:F.315, B:F.316, A:L.312, A:F.315 PGT.7: 12 residues within 4Å: Chain B: A.89, A.90, S.91, R.366 Chain C: F.84, S.91, K.92, Y.521 Ligands: PGT.3, PGT.4, PGT.10, PGT.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.90, C:Y.521 Salt bridges: B:R.366 PGT.10: 12 residues within 4Å: Chain B: F.83, F.84, V.86, V.87, A.90, S.91, V.512, K.513, S.516, Y.521 Ligands: PGT.3, PGT.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.83, B:F.83, B:F.83, B:V.86, B:V.87, B:A.90 PGT.16: 14 residues within 4Å: Chain C: S.111, S.114, F.117, M.121, N.278, M.281, V.282, A.284, A.285, A.288, I.289, V.382, W.383 Ligands: PGT.17 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.117, C:M.281, C:V.282, C:A.284, C:A.285, C:A.288, C:I.289, C:V.382, C:W.383 Hydrogen bonds: C:N.278 PGT.17: 7 residues within 4Å: Chain A: A.65, N.69 Chain C: V.293, V.294, G.295, T.297 Ligands: PGT.16 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.297 Hydrogen bonds: C:T.297, C:T.297, C:T.297 PGT.18: 5 residues within 4Å: Chain C: F.509, V.512, K.513 Ligands: PGT.7, CM5.19 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.509, C:F.509, C:F.509, C:V.512, C:K.513, C:K.513 Salt bridges: C:K.513

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 6 residues within 4Å: Chain B: A.118, Q.274, S.277, F.355, T.438, S.442 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.277, B:S.442, B:S.442

1 x CM5: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE(Non-covalent)

CM5.19: 8 residues within 4Å: Chain C: F.192, L.195, I.196, K.199, L.205, I.209, F.502 Ligands: PGT.18 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.192, C:I.196, C:L.205, C:I.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koshy, C. et al., Structural Evidence for Functional Lipid Interactions in the Betaine Transporter Betp. Embo J. (2013)

Release Date

2013-10-30

Peptides

GLYCINE BETAINE TRANSPORTER BETP: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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GLYCINE BETAINE TRANSPORTER BETP

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