SMTL ID : 8jf2.1

Cryo-EM structure of tetrameric DltB/DltC complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

PGT.1: 8 residues within 4Å: Chain A: K.116, Y.120, S.123, V.127, V.159, I.163, V.325, F.359 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.120, A:Y.120, A:Y.120, A:V.325 PGT.7: 16 residues within 4Å: Chain B: F.119, Y.120, V.127, L.130, I.131, K.134, F.156, I.163, R.166, W.320, R.328, V.356, F.359, W.360, I.363 Chain F: R.52 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.119, B:Y.120, B:Y.120, B:V.127, B:I.131, B:F.156, B:I.163, B:W.320 PGT.16: 10 residues within 4Å: Chain A: L.53, I.57, F.61 Chain B: F.61 Ligands: LMT.2, LMT.4, LMT.8, LMT.9, LMT.27, LMT.31 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.53, A:I.57, A:F.61, A:F.61, A:F.61 PGT.17: 15 residues within 4Å: Chain C: F.119, Y.120, L.130, I.131, K.134, V.135, F.156, R.166, V.325, R.328, L.329, R.335, F.359, W.360, I.363 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.119, C:Y.120, C:F.156, C:V.325, C:L.329 Hydrogen bonds: C:F.359 PGT.25: 8 residues within 4Å: Chain C: I.57, F.61 Chain D: L.53 Ligands: LMT.8, LMT.19, LMT.20, LMT.27, LMT.28 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.53, C:I.57, C:F.61 PGT.26: 14 residues within 4Å: Chain D: Y.120, V.127, L.130, I.131, K.134, F.156, I.163, W.320, V.325, R.328, V.356, F.359, W.360 Chain H: R.52 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.120, D:Y.120, D:V.127, D:I.131, D:I.163, D:W.320, D:V.325 Hydrogen bonds: D:L.130

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

LMT.2: 5 residues within 4Å: Chain A: F.60, F.61 Chain B: I.57 Ligands: LMT.12, PGT.16 Ligand excluded by PLIP LMT.3: 9 residues within 4Å: Chain A: G.40, F.231, V.232, Q.235 Chain B: L.30, L.33, I.89 Ligands: LMT.5, DGA.6 Ligand excluded by PLIP LMT.4: 10 residues within 4Å: Chain A: P.54, I.57, G.58, F.61, K.62, K.63, F.65 Ligands: PGT.16, LMT.29, LMT.31 Ligand excluded by PLIP LMT.5: 7 residues within 4Å: Chain A: P.34, H.35, L.36, Y.47, I.50, L.79 Ligands: LMT.3 Ligand excluded by PLIP LMT.8: 5 residues within 4Å: Ligands: LMT.9, LMT.10, PGT.16, PGT.25, LMT.27 Ligand excluded by PLIP LMT.9: 8 residues within 4Å: Chain B: F.56, I.57, F.60, F.61, R.209 Ligands: LMT.8, LMT.10, PGT.16 Ligand excluded by PLIP LMT.10: 5 residues within 4Å: Chain B: L.213 Ligands: LMT.8, LMT.9, LMT.11, LMT.20 Ligand excluded by PLIP LMT.11: 8 residues within 4Å: Chain B: D.210, L.213, N.214, E.217 Chain C: K.63, F.65 Ligands: LMT.10, LMT.20 Ligand excluded by PLIP LMT.12: 10 residues within 4Å: Chain A: F.56, I.57, F.60, L.213, L.216 Chain B: I.57, F.61, K.63, F.65 Ligands: LMT.2 Ligand excluded by PLIP LMT.13: 8 residues within 4Å: Chain B: K.221, Y.229, F.272, F.297, K.299 Chain C: I.67, I.74 Ligands: LMT.24 Ligand excluded by PLIP LMT.14: 4 residues within 4Å: Chain B: P.34, H.35, L.79 Ligands: DGA.6 Ligand excluded by PLIP LMT.15: 5 residues within 4Å: Chain B: E.37, G.40, P.42, V.232, Q.235 Ligand excluded by PLIP LMT.19: 7 residues within 4Å: Chain C: I.57, K.62, R.209 Chain D: F.61 Ligands: LMT.20, LMT.21, PGT.25 Ligand excluded by PLIP LMT.20: 10 residues within 4Å: Chain C: P.54, I.57, F.61, K.62, K.63, F.65 Ligands: LMT.10, LMT.11, LMT.19, PGT.25 Ligand excluded by PLIP LMT.21: 9 residues within 4Å: Chain C: F.56, F.60, R.209, L.216 Chain D: I.57, F.61, K.63, F.65 Ligands: LMT.19 Ligand excluded by PLIP LMT.22: 6 residues within 4Å: Chain C: P.42, F.231, V.232, Q.235 Chain D: Q.32 Ligands: DGA.18 Ligand excluded by PLIP LMT.23: 5 residues within 4Å: Chain C: P.34, H.35, Y.47, A.51, L.79 Ligand excluded by PLIP LMT.24: 6 residues within 4Å: Chain C: A.66, I.74, T.174, L.179, L.183 Ligands: LMT.13 Ligand excluded by PLIP LMT.27: 5 residues within 4Å: Ligands: LMT.8, PGT.16, PGT.25, LMT.28, LMT.31 Ligand excluded by PLIP LMT.28: 8 residues within 4Å: Chain D: L.53, I.57, F.60, F.61, R.209 Ligands: PGT.25, LMT.27, LMT.31 Ligand excluded by PLIP LMT.29: 8 residues within 4Å: Chain A: K.63, F.65 Chain D: D.210, L.213, E.217, V.220 Ligands: LMT.4, LMT.31 Ligand excluded by PLIP LMT.30: 13 residues within 4Å: Chain D: R.304, D.305, M.306, E.308, F.373, G.377, N.381, W.384, L.385, K.388, T.409, G.413, T.420 Ligand excluded by PLIP LMT.31: 6 residues within 4Å: Chain D: L.213 Ligands: LMT.4, PGT.16, LMT.27, LMT.28, LMT.29 Ligand excluded by PLIP LMT.32: 10 residues within 4Å: Chain A: I.67, C.70 Chain D: K.221, L.225, Y.229, F.272, M.280, D.298, K.299, P.300 Ligand excluded by PLIP LMT.33: 6 residues within 4Å: Chain D: P.34, H.35, N.41, A.51, L.79 Ligands: DGA.18 Ligand excluded by PLIP

2 x DGA: DIACYL GLYCEROL(Non-covalent)

DGA.6: 12 residues within 4Å: Chain A: P.42, I.46, I.223, F.227, L.228 Chain B: L.71, I.74, T.75, V.78, L.79 Ligands: LMT.3, LMT.14 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.46, A:I.223, A:F.227, A:L.228, B:L.71, B:I.74 DGA.18: 16 residues within 4Å: Chain C: P.42, I.46, G.49, L.53, F.56, L.216, I.223, M.224, F.227 Chain D: P.34, I.74, T.75, V.78, L.79 Ligands: LMT.22, LMT.33 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.42, C:I.46, C:L.53, C:L.53, C:F.56, C:L.216, C:I.223, C:F.227, C:F.227, 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
D-alanyl carrier protein: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
G

G
H

H
I

Membrane

We predict this structure to be a membrane protein.
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Teichoic acid D-alanyltransferase

D-alanyl carrier protein

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