- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-tetramer
- Ligands
- 4 x ASW: N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide(Non-covalent)
- 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 PLIPLMT.5: 6 residues within 4Å:- Chain A: P.34, H.35, A.51, F.76, L.79
- Ligands: LMT.43
Ligand excluded by PLIPLMT.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 PLIPLMT.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 PLIPLMT.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 PLIPLMT.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 PLIPLMT.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 PLIPLMT.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 PLIPLMT.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 PLIPLMT.16: 5 residues within 4Å:- Chain B: P.42, F.43, I.46, I.223
- Ligands: LMT.15
Ligand excluded by PLIPLMT.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 PLIPLMT.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 PLIPLMT.20: 4 residues within 4Å:- Chain B: V.325, L.329, N.336
- Ligands: PGT.13
Ligand excluded by PLIPLMT.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 PLIPLMT.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 PLIPLMT.23: 7 residues within 4Å:- Ligands: LMT.9, PGT.11, LMT.24, LMT.25, LMT.36, PGT.38, LMT.50
Ligand excluded by PLIPLMT.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 PLIPLMT.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 PLIPLMT.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 PLIPLMT.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 PLIPLMT.30: 6 residues within 4Å:- Chain C: P.34, H.35, L.36, T.75, L.79
- Ligands: LMT.35
Ligand excluded by PLIPLMT.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 PLIPLMT.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 PLIPLMT.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 PLIPLMT.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 PLIPLMT.36: 6 residues within 4Å:- Chain C: F.61
- Ligands: LMT.23, LMT.25, LMT.37, PGT.38, LMT.50
Ligand excluded by PLIPLMT.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 PLIPLMT.41: 4 residues within 4Å:- Chain D: V.325, L.329, V.338
- Ligands: PGT.40
Ligand excluded by PLIPLMT.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 PLIPLMT.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 PLIPLMT.44: 4 residues within 4Å:- Chain D: F.43, F.227
- Ligands: PGT.38, LMT.43
Ligand excluded by PLIPLMT.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 PLIPLMT.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 PLIPLMT.48: 6 residues within 4Å:- Chain D: Y.229, L.233, F.273, K.299, I.302
- Ligands: LMT.49
Ligand excluded by PLIPLMT.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 PLIPLMT.50: 7 residues within 4Å:- Ligands: LMT.9, PGT.11, LMT.23, LMT.36, PGT.38, LMT.51, LMT.53
Ligand excluded by PLIPLMT.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 PLIPLMT.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 PLIPLMT.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 PLIPLMT.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
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-tetramer
- Ligands
- 4 x ASW: N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide(Non-covalent)
- 8 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)
- 40 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)(Non-functional Binders)
- 2 x DGA: DIACYL GLYCEROL(Non-covalent)
- 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
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.