SMTL ID : 9gkk.1

BetP heterotrimeric complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.04 Å

Oligo State

homo-trimer

Ligands

3 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: A.155, M.158, G.159, F.472, T.475, S.476 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.472, A:S.476 NA.5: 6 residues within 4Å: Chain B: A.155, M.158, G.159, F.472, T.475, S.476 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.472, B:S.476 NA.9: 5 residues within 4Å: Chain C: A.155, M.158, F.472, T.475, S.476 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.475, C:S.476

3 x BET: TRIMETHYL GLYCINE(Non-covalent)

BET.2: 10 residues within 4Å: Chain A: G.157, M.158, G.159, I.160, G.161, Y.205, S.261, W.381, W.382, W.385 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.159, A:I.160, A:S.261 pi-Cation interactions: A:W.381, A:W.381, A:W.382, A:W.382, A:W.385, A:W.385 BET.6: 9 residues within 4Å: Chain B: G.157, G.159, I.160, G.161, Y.205, S.261, W.381, W.382, W.385 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.159, B:I.160, B:I.160, B:S.261 pi-Cation interactions: B:W.381, B:W.381, B:W.382, B:W.382, B:W.385, B:W.385 BET.11: 9 residues within 4Å: Chain C: G.157, M.158, G.159, I.160, G.161, Y.205, W.381, W.382, W.385 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.159, C:I.160, C:G.161 pi-Cation interactions: C:W.381, C:W.381, C:W.382, C:W.382, C:W.385, C:W.385

2 x XKJ: dodecyl beta-D-glucopyranoside(Non-covalent)

XKJ.3: 12 residues within 4Å: Chain A: L.113, T.116, V.117, F.120, V.124, I.125, S.128, F.130, A.356 Chain C: P.342, I.345 Ligands: PGT.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.113, A:T.116, A:F.120, A:F.120, C:I.345 Hydrogen bonds: A:S.128 XKJ.12: 11 residues within 4Å: Chain C: V.123, L.199, L.349, S.350, F.352, F.353, L.407, L.410, L.411 Ligands: CDL.4, PGT.10 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.199, C:L.349, C:F.352

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 24 residues within 4Å: Chain A: F.120, A.126, A.127, M.194, I.345, F.353, R.403, L.407, L.411, G.415, T.418 Chain B: F.120, V.123, V.124, A.127, S.128, K.129, L.349, F.352 Chain C: L.349 Ligands: PGT.7, LMT.8, PGT.10, XKJ.12 20 PLIP interactions: 12 interactions with chain A, 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:F.120, A:A.127, A:I.345, A:F.353, A:F.353, A:L.407, A:L.407, A:L.411, A:L.411, B:F.120, B:F.120, B:V.123, B:A.127, B:L.349, B:F.352, C:L.349 Hydrogen bonds: A:R.403 Salt bridges: A:R.403, A:R.403, B:K.129

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

PGT.7: 12 residues within 4Å: Chain B: V.123, A.127, M.194, T.198, I.345, Y.348, F.353, R.403, T.418 Chain C: A.127 Ligands: CDL.4, PGT.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.123, B:M.194, B:T.198, B:I.345, B:Y.348, B:Y.348, B:F.353, B:T.418 Salt bridges: B:R.403 PGT.10: 19 residues within 4Å: Chain A: F.120, V.123, V.124, A.127, S.128, K.129, L.349, F.352, F.353 Chain C: L.199, R.403, L.407, L.411, A.414, T.418 Ligands: XKJ.3, CDL.4, PGT.7, XKJ.12 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:F.120, A:F.120, A:F.120, A:V.123, A:V.124, A:L.349, A:F.352, A:F.352, A:F.353, C:L.199, C:L.411, C:A.414 Hydrogen bonds: A:K.129, C:R.403 Salt bridges: C:R.403

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.8: 15 residues within 4Å: Chain A: P.342, I.345 Chain B: T.116, V.117, F.120, F.121, V.124, I.125, S.128, K.129, F.130, A.356, V.549, S.553 Ligands: CDL.4 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.117, B:F.120, B:F.120, B:F.120, B:A.356, A:I.345 Hydrogen bonds: B:S.128, B:S.128, B:K.129, B:S.553 Salt bridges: B:K.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Urbansky, K. et al., Structure of Glycine betaine transporter BetP heterotrimeric complex. To be published

Release Date

2025-09-10

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