SMTL ID : 8jem.1

DltB tetramer in complex with inhibitor m-AMSA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ASW: N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide(Non-covalent)

ASW.1: 14 residues within 4Å: Chain A: Y.153, S.190, Y.267, L.271, D.274, F.275, Y.278, W.310, W.313, H.314, M.357, W.360, H.361, Y.370 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.271, A:F.275, A:F.275, A:F.275, A:Y.278, A:Y.278 Hydrogen bonds: A:H.314, A:H.361 ASW.12: 13 residues within 4Å: Chain B: Y.153, S.190, Y.267, L.271, D.274, F.275, Y.278, W.310, W.313, H.314, M.357, H.361, Y.370 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.271, B:F.275, B:Y.278 Hydrogen bonds: B:H.314, B:H.361 ASW.28: 13 residues within 4Å: Chain C: Y.153, S.190, Y.267, L.271, D.274, F.275, Y.278, W.310, W.313, H.314, W.360, H.361, Y.370 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.271, C:F.275, C:F.275, C:Y.278, C:Y.278 Hydrogen bonds: C:H.314, C:H.361 ASW.39: 14 residues within 4Å: Chain D: Y.153, S.190, Y.267, L.271, D.274, F.275, Y.278, W.310, W.313, H.314, M.357, W.360, H.361, Y.370 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.271, D:F.275, D:Y.278, D:W.360 Hydrogen bonds: D:H.314, D:H.361

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

PGT.2: 16 residues within 4Å: Chain A: K.116, F.119, Y.120, V.127, L.130, I.131, K.134, F.156, I.163, R.328, L.329, R.335, V.356, F.359, W.360, I.363 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.116, A:F.119, A:F.119, A:Y.120, A:V.127, A:I.163, A:R.328, A:L.329 Hydrogen bonds: A:F.359 PGT.11: 15 residues within 4Å: Chain A: L.53, I.57, F.61, R.209 Chain B: I.50, L.53, I.57, F.61 Ligands: DGA.4, LMT.8, LMT.9, LMT.23, LMT.24, LMT.27, LMT.50 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:I.57, A:F.61 Hydrogen bonds: A:R.209 Salt bridges: A:R.209 PGT.13: 22 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, W.320, V.325, R.328, V.332, R.335, V.356, F.359, W.360, I.363 Ligands: LMT.20 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.127, B:V.127, B:F.156, B:I.163, B:W.320, B:V.325, B:V.332 Hydrogen bonds: B:F.359 PGT.17: 11 residues within 4Å: Chain B: C.70, I.74, V.78, L.92, L.93, I.96, K.107, R.108, E.172, L.175 Ligands: LMT.18 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.74, B:V.78, B:L.92, B:L.93, B:L.175 Salt bridges: B:R.108 PGT.29: 17 residues within 4Å: Chain C: F.119, Y.120, S.123, V.127, L.130, I.131, K.134, F.156, R.166, W.320, V.325, R.328, V.332, R.335, F.359, W.360, I.363 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.119, C:Y.120, C:Y.120, C:V.127, C:I.131, C:F.156, C:W.320, C:V.325 Hydrogen bonds: C:F.359 PGT.38: 19 residues within 4Å: Chain C: L.53, I.57, F.60, R.209 Chain D: I.46, I.50, L.53, P.54, I.57, F.61, Y.68 Ligands: LMT.23, DGA.32, LMT.35, LMT.36, LMT.44, LMT.50, LMT.51, LMT.54 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.53, C:I.57, C:F.60, D:I.46, D:I.50, D:P.54, D:I.57 Hydrogen bonds: C:R.209 Salt bridges: C:R.209, C:R.209 PGT.40: 18 residues within 4Å: Chain D: K.116, F.119, Y.120, V.127, L.130, I.131, K.134, F.156, R.166, W.320, V.325, R.328, V.332, R.335, N.336, V.356, F.359 Ligands: LMT.41 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.119, D:F.119, D:Y.120, D:V.127, D:V.127, D:F.156, D:W.320, D:V.325, D:V.332 Hydrogen bonds: D:I.131 PGT.45: 11 residues within 4Å: Chain D: I.74, L.93, V.97, Y.104, K.107, R.108, F.173, L.175, L.179 Ligands: DGA.32, LMT.46 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.93, D:V.97, D:L.179 Hydrogen bonds: D:K.107, D:K.107 Salt bridges: D:K.107, D:R.108

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

LMT.3: 12 residues within 4Å: Chain A: G.40, N.41, P.42, F.43, F.231, V.232, Q.235 Chain B: F.29, L.30, Q.32, L.93 Ligands: DGA.4 Ligand excluded by PLIP LMT.5: 6 residues within 4Å: Chain A: P.34, H.35, A.51, F.76, L.79 Ligands: LMT.43 Ligand excluded by PLIP LMT.6: 15 residues within 4Å: Chain A: R.304, D.305, M.306, F.373, G.377, N.381, W.384, L.385, K.388, L.403, P.404, E.405, T.409, T.417, T.420 Ligand excluded by PLIP LMT.7: 9 residues within 4Å: Chain A: A.66, I.74, L.93, I.96, T.174, G.176, L.179, R.180 Ligands: LMT.49 Ligand excluded by PLIP LMT.8: 6 residues within 4Å: Chain A: F.43 Chain B: Y.47, I.50 Ligands: DGA.4, PGT.11, LMT.14 Ligand excluded by PLIP LMT.9: 7 residues within 4Å: Chain A: L.53, F.61 Ligands: LMT.10, PGT.11, LMT.23, LMT.50, LMT.53 Ligand excluded by PLIP LMT.10: 10 residues within 4Å: Chain A: P.54, I.57, G.58, F.61, K.62, K.63, F.65 Ligands: LMT.9, LMT.52, LMT.53 Ligand excluded by PLIP LMT.14: 7 residues within 4Å: Chain B: P.34, H.35, L.71, T.75, L.79 Ligands: DGA.4, LMT.8 Ligand excluded by PLIP LMT.15: 7 residues within 4Å: Chain B: G.40, N.41, P.42, F.231, V.232, Q.235 Ligands: LMT.16 Ligand excluded by PLIP LMT.16: 5 residues within 4Å: Chain B: P.42, F.43, I.46, I.223 Ligands: LMT.15 Ligand excluded by PLIP LMT.18: 7 residues within 4Å: Chain B: I.100, Y.104, S.105, R.108, Y.109, Q.112 Ligands: PGT.17 Ligand excluded by PLIP LMT.19: 16 residues within 4Å: Chain B: R.304, D.305, M.306, F.373, G.377, I.380, W.384, L.385, K.388, L.403, P.404, E.405, T.409, G.413, I.416, T.420 Ligand excluded by PLIP LMT.20: 4 residues within 4Å: Chain B: V.325, L.329, N.336 Ligands: PGT.13 Ligand excluded by PLIP LMT.21: 9 residues within 4Å: Chain B: L.228, Y.229, F.272, F.297, D.298, K.299 Chain C: I.67, L.71 Ligands: LMT.22 Ligand excluded by PLIP LMT.22: 7 residues within 4Å: Chain B: Y.229, L.233, F.237, K.299, I.302 Ligands: LMT.21, LMT.34 Ligand excluded by PLIP LMT.23: 7 residues within 4Å: Ligands: LMT.9, PGT.11, LMT.24, LMT.25, LMT.36, PGT.38, LMT.50 Ligand excluded by PLIP LMT.24: 8 residues within 4Å: Chain B: L.53, I.57, F.60, F.61, R.209 Ligands: PGT.11, LMT.23, LMT.25 Ligand excluded by PLIP LMT.25: 8 residues within 4Å: Chain B: R.209, D.210, L.213 Ligands: LMT.23, LMT.24, LMT.26, LMT.36, LMT.37 Ligand excluded by PLIP LMT.26: 9 residues within 4Å: Chain B: N.214, L.216, E.217, V.220 Chain C: P.54, K.63, F.65 Ligands: LMT.25, LMT.37 Ligand excluded by PLIP LMT.27: 13 residues within 4Å: Chain A: I.57, F.60, R.209, D.210, L.213, L.216 Chain B: I.57, F.61, K.62, K.63, F.65 Ligands: DGA.4, PGT.11 Ligand excluded by PLIP LMT.30: 6 residues within 4Å: Chain C: P.34, H.35, L.36, T.75, L.79 Ligands: LMT.35 Ligand excluded by PLIP LMT.31: 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.90, L.93 Ligands: DGA.32 Ligand excluded by PLIP LMT.33: 11 residues within 4Å: Chain C: R.304, D.305, G.377, N.381, W.384, L.385, K.388, T.409, G.413, T.417, T.420 Ligand excluded by PLIP LMT.34: 7 residues within 4Å: Chain C: R.64, I.74, I.96, T.174, G.176, R.180 Ligands: LMT.22 Ligand excluded by PLIP LMT.35: 8 residues within 4Å: Chain C: F.43, I.46 Chain D: Y.47, I.50 Ligands: LMT.30, DGA.32, PGT.38, LMT.42 Ligand excluded by PLIP LMT.36: 6 residues within 4Å: Chain C: F.61 Ligands: LMT.23, LMT.25, LMT.37, PGT.38, LMT.50 Ligand excluded by PLIP LMT.37: 9 residues within 4Å: Chain B: L.213 Chain C: P.54, I.57, F.61, K.62, K.63 Ligands: LMT.25, LMT.26, LMT.36 Ligand excluded by PLIP LMT.41: 4 residues within 4Å: Chain D: V.325, L.329, V.338 Ligands: PGT.40 Ligand excluded by PLIP LMT.42: 9 residues within 4Å: Chain C: F.43 Chain D: L.33, P.34, H.35, L.36, A.51, T.75, L.79 Ligands: LMT.35 Ligand excluded by PLIP LMT.43: 7 residues within 4Å: Chain A: L.71 Chain D: N.41, P.42, F.231, Q.235 Ligands: LMT.5, LMT.44 Ligand excluded by PLIP LMT.44: 4 residues within 4Å: Chain D: F.43, F.227 Ligands: PGT.38, LMT.43 Ligand excluded by PLIP LMT.46: 8 residues within 4Å: Chain D: I.100, I.101, S.105, R.108, Y.109, Q.112, R.113 Ligands: PGT.45 Ligand excluded by PLIP LMT.47: 15 residues within 4Å: Chain D: R.304, D.305, M.306, E.308, F.373, I.376, G.377, W.384, L.385, K.388, E.405, G.413, I.416, T.417, T.420 Ligand excluded by PLIP LMT.48: 6 residues within 4Å: Chain D: Y.229, L.233, F.273, K.299, I.302 Ligands: LMT.49 Ligand excluded by PLIP LMT.49: 14 residues within 4Å: Chain A: I.67, C.70, L.71, I.74 Chain D: K.221, L.225, L.228, Y.229, F.272, M.280, F.297, K.299 Ligands: LMT.7, LMT.48 Ligand excluded by PLIP LMT.50: 7 residues within 4Å: Ligands: LMT.9, PGT.11, LMT.23, LMT.36, PGT.38, LMT.51, LMT.53 Ligand excluded by PLIP LMT.51: 10 residues within 4Å: Chain D: L.53, I.57, F.60, F.61, K.62, R.209 Ligands: PGT.38, LMT.50, LMT.53, LMT.54 Ligand excluded by PLIP LMT.52: 9 residues within 4Å: Chain A: K.63, F.65 Chain D: D.210, L.213, N.214, E.217, V.220 Ligands: LMT.10, LMT.53 Ligand excluded by PLIP LMT.53: 8 residues within 4Å: Chain D: R.209, D.210, L.213 Ligands: LMT.9, LMT.10, LMT.50, LMT.51, LMT.52 Ligand excluded by PLIP LMT.54: 9 residues within 4Å: Chain C: F.60, L.213 Chain D: P.54, F.61, K.63, F.65 Ligands: DGA.32, PGT.38, LMT.51 Ligand excluded by PLIP

2 x DGA: DIACYL GLYCEROL(Non-covalent)

DGA.4: 22 residues within 4Å: Chain A: P.42, F.43, F.45, I.46, L.53, L.216, 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.3, LMT.8, PGT.11, LMT.14, LMT.27 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.42, A:I.46, A:L.53, A:L.216, A:L.216, A:I.223, A:F.227, A:L.228, A:L.288, B:P.54 DGA.32: 20 residues within 4Å: Chain C: F.43, F.45, I.46, 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.31, LMT.35, PGT.38, PGT.45, LMT.54 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.45, C:F.56, C:L.216, C:L.216, C:I.223, 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

2024-05-15

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.
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Teichoic acid D-alanyltransferase

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