SMTL ID : 8jes.1

Cryo-EM structure of DltB homo-tetramer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

PGT.1: 19 residues within 4Å: Chain A: K.116, F.119, Y.120, S.123, L.130, I.131, K.134, V.135, F.156, V.159, I.163, W.320, R.328, L.329, N.336, V.356, F.359, W.360, I.363 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.116, A:F.119, A:F.119, A:F.156, A:V.159, A:I.163, A:W.320, A:L.329 PGT.9: 12 residues within 4Å: Chain A: L.53, F.60, R.209 Chain B: I.50, L.53, I.57, F.61 Ligands: LMT.7, LMT.18, LMT.19, LMT.22, LMT.39 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.53, B:I.57, A:L.53, A:L.53, A:F.60 Hydrogen bonds: A:R.209 Salt bridges: A:R.209 PGT.10: 21 residues within 4Å: Chain B: K.116, F.119, Y.120, S.123, V.127, L.130, I.131, K.134, V.135, F.156, I.163, R.166, V.325, R.328, V.332, R.335, V.356, F.359, W.360, I.363 Ligands: LMT.15 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.120, B:Y.120, B:V.127, B:V.127, B:I.131, B:F.156, B:I.163, B:V.325, B:V.332 Hydrogen bonds: B:F.359 PGT.23: 19 residues within 4Å: Chain C: W.117, Y.120, S.123, V.127, L.130, I.131, K.134, V.135, F.156, V.159, I.163, W.320, F.324, R.328, V.332, R.335, F.359, W.360, I.363 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.117, C:Y.120, C:V.127, C:F.156, C:V.159, C:I.163, C:W.320 PGT.30: 13 residues within 4Å: Chain C: L.53, I.57, F.60, R.209 Chain D: I.46, I.50, L.53, F.61 Ligands: LMT.18, LMT.28, LMT.39, LMT.40, LMT.43 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.53, C:I.57, C:F.60, D:I.46, D:I.50 Hydrogen bonds: C:R.209 Salt bridges: C:R.209, C:R.209 PGT.32: 21 residues within 4Å: Chain D: K.116, F.119, Y.120, V.127, L.130, I.131, K.134, V.135, F.156, I.163, R.166, W.320, F.321, V.325, R.328, R.335, N.336, V.356, F.359, I.363 Ligands: LMT.33 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.119, D:Y.120, D:V.127, D:V.127, D:F.156, D:I.163, D:W.320, D:V.325, D:R.328

35 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)(Non-functional Binders)

LMT.2: 9 residues within 4Å: Chain A: P.42, F.231, V.232, Q.235 Chain B: F.29, L.30, Q.32, L.93 Ligands: DGA.3 Ligand excluded by PLIP LMT.4: 5 residues within 4Å: Chain A: P.34, H.35, A.51, V.72, L.79 Ligand excluded by PLIP LMT.5: 14 residues within 4Å: Chain A: R.304, D.305, M.306, F.373, N.381, W.384, L.385, K.388, N.392, L.403, P.404, E.405, T.409, T.420 Ligand excluded by PLIP LMT.6: 7 residues within 4Å: Chain A: A.66, I.74, T.174, G.176, E.177, L.179 Ligands: LMT.38 Ligand excluded by PLIP LMT.7: 8 residues within 4Å: Chain A: L.53, I.57, F.61 Ligands: LMT.8, PGT.9, LMT.18, LMT.39, LMT.42 Ligand excluded by PLIP LMT.8: 9 residues within 4Å: Chain A: P.54, I.57, G.58, F.61, K.62 Chain D: L.213 Ligands: LMT.7, LMT.41, LMT.42 Ligand excluded by PLIP LMT.11: 7 residues within 4Å: Chain A: F.43, I.46 Chain B: P.34, H.35, Y.68, L.79 Ligands: DGA.3 Ligand excluded by PLIP LMT.12: 7 residues within 4Å: Chain B: G.40, P.42, F.231, V.232, Q.235 Chain C: T.75 Ligands: LMT.13 Ligand excluded by PLIP LMT.13: 6 residues within 4Å: Chain B: N.41, P.42, F.43, I.46, I.223 Ligands: LMT.12 Ligand excluded by PLIP LMT.14: 16 residues within 4Å: Chain B: R.304, D.305, M.306, F.373, I.376, G.377, I.380, W.384, K.388, L.403, P.404, E.405, T.409, G.413, I.416, T.420 Ligand excluded by PLIP LMT.15: 4 residues within 4Å: Chain B: V.325, L.329, N.336 Ligands: PGT.10 Ligand excluded by PLIP LMT.16: 13 residues within 4Å: Chain B: K.221, Y.222, L.225, L.228, Y.229, F.272, F.297, D.298, K.299 Chain C: I.67, L.71 Ligands: LMT.17, LMT.27 Ligand excluded by PLIP LMT.17: 6 residues within 4Å: Chain B: Y.229, F.237, K.299, I.302 Ligands: LMT.16, LMT.27 Ligand excluded by PLIP LMT.18: 7 residues within 4Å: Ligands: LMT.7, PGT.9, LMT.19, LMT.20, LMT.28, PGT.30, LMT.39 Ligand excluded by PLIP LMT.19: 8 residues within 4Å: Chain B: L.53, I.57, F.60, F.61, R.209 Ligands: PGT.9, LMT.18, LMT.20 Ligand excluded by PLIP LMT.20: 9 residues within 4Å: Chain B: R.209, D.210, L.213, L.216 Ligands: LMT.18, LMT.19, LMT.21, LMT.28, LMT.29 Ligand excluded by PLIP LMT.21: 10 residues within 4Å: Chain B: D.210, L.213, N.214, E.217, V.220 Chain C: P.54, K.63, F.65 Ligands: LMT.20, LMT.29 Ligand excluded by PLIP LMT.22: 15 residues within 4Å: Chain A: F.56, I.57, F.60, R.209, D.210, L.213, L.216 Chain B: I.57, G.58, F.61, K.62, K.63, F.65 Ligands: DGA.3, PGT.9 Ligand excluded by PLIP LMT.24: 7 residues within 4Å: Chain C: P.34, H.35, L.36, A.51, T.75, L.79 Ligands: LMT.25 Ligand excluded by PLIP LMT.25: 13 residues within 4Å: Chain C: N.41, P.42, F.231, V.232, Q.235 Chain D: M.26, F.29, L.30, Q.32, L.33, L.93 Ligands: LMT.24, DGA.31 Ligand excluded by PLIP LMT.26: 10 residues within 4Å: Chain C: R.304, D.305, M.306, F.373, N.381, W.384, L.385, K.388, I.416, T.420 Ligand excluded by PLIP LMT.27: 9 residues within 4Å: Chain C: R.64, I.74, T.174, G.176, E.177, L.179, L.183 Ligands: LMT.16, LMT.17 Ligand excluded by PLIP LMT.28: 6 residues within 4Å: Chain C: F.61 Ligands: LMT.18, LMT.20, LMT.29, PGT.30, LMT.39 Ligand excluded by PLIP LMT.29: 7 residues within 4Å: Chain B: L.213 Chain C: P.54, I.57, F.61 Ligands: LMT.20, LMT.21, LMT.28 Ligand excluded by PLIP LMT.33: 5 residues within 4Å: Chain D: V.325, L.329, V.332, V.338 Ligands: PGT.32 Ligand excluded by PLIP LMT.34: 9 residues within 4Å: Chain C: F.43 Chain D: Q.32, L.33, P.34, H.35, L.36, Y.47, A.51, L.79 Ligand excluded by PLIP LMT.35: 6 residues within 4Å: Chain A: L.71, T.75 Chain D: N.41, P.42, F.231, Q.235 Ligand excluded by PLIP LMT.36: 13 residues within 4Å: Chain D: R.304, D.305, M.306, F.373, I.376, G.377, I.380, W.384, L.385, K.388, G.413, I.416, T.420 Ligand excluded by PLIP LMT.37: 5 residues within 4Å: Chain D: Y.229, L.233, K.299, I.302 Ligands: LMT.38 Ligand excluded by PLIP LMT.38: 12 residues within 4Å: Chain A: I.67, I.74 Chain D: K.221, L.225, Y.229, F.272, M.280, F.297, D.298, K.299 Ligands: LMT.6, LMT.37 Ligand excluded by PLIP LMT.39: 7 residues within 4Å: Ligands: LMT.7, PGT.9, LMT.18, LMT.28, PGT.30, LMT.40, LMT.42 Ligand excluded by PLIP LMT.40: 10 residues within 4Å: Chain D: L.53, I.57, F.60, F.61, K.62, R.209 Ligands: PGT.30, LMT.39, LMT.42, LMT.43 Ligand excluded by PLIP LMT.41: 9 residues within 4Å: Chain A: K.63, F.65 Chain D: D.210, L.213, N.214, E.217, V.220 Ligands: LMT.8, LMT.42 Ligand excluded by PLIP LMT.42: 8 residues within 4Å: Chain D: R.209, D.210, L.213 Ligands: LMT.7, LMT.8, LMT.39, LMT.40, LMT.41 Ligand excluded by PLIP LMT.43: 10 residues within 4Å: Chain C: F.60, L.213 Chain D: P.54, I.57, F.61, K.63, F.65 Ligands: PGT.30, DGA.31, LMT.40 Ligand excluded by PLIP

2 x DGA: DIACYL GLYCEROL(Non-covalent)

DGA.3: 18 residues within 4Å: Chain A: P.42, I.46, L.216, V.220, I.223, M.224, F.227, L.228, L.288 Chain B: P.34, P.54, I.74, T.75, V.78, L.79 Ligands: LMT.2, LMT.11, LMT.22 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.42, A:I.46, A:L.216, A:V.220, A:I.223, A:F.227, A:L.228, A:L.288, B:P.54 DGA.31: 18 residues within 4Å: Chain C: F.43, F.45, I.46, G.49, L.53, F.56, L.216, I.223, M.224, F.227, L.228 Chain D: P.34, I.74, T.75, V.78, L.79 Ligands: LMT.25, LMT.43 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.45, C:L.53, C:F.56, C:F.56, C:L.216, C:I.223, C:F.227, C:F.227, C:F.227, C:L.228, D:I.74, D:T.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, P. et al., Structural insights into the transporting and catalyzing mechanism of DltB in LTA D-alanylation. Nat Commun (2024)

Release Date

2024-05-22

Peptides

Teichoic acid D-alanyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Teichoic acid D-alanyltransferase

Related Entries With Identical Sequence