SMTL ID : 7xs6.1

structure of a membrane-integrated glycosyltransferase with inhibitor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

16 x C14: TETRADECANE(Non-covalent)

C14.1: 5 residues within 4Å: Chain A: V.836, W.840 Chain B: I.1064, Y.1067, K.1071 Ligand excluded by PLIP C14.2: 4 residues within 4Å: Chain A: A.830, V.833, I.837, F.838 Ligand excluded by PLIP C14.3: 5 residues within 4Å: Chain A: F.831, I.877, Y.878, F.881, F.885 Ligand excluded by PLIP C14.4: 8 residues within 4Å: Chain A: N.644, P.645, E.748, R.749, V.866, C.869, A.873, L.948 Ligand excluded by PLIP C14.5: 6 residues within 4Å: Chain A: S.848, T.861, F.864 Chain B: L.1042, I.1045, I.1049 Ligand excluded by PLIP C14.6: 5 residues within 4Å: Chain A: V.1057, I.1064, K.1093 Chain B: W.840 Ligands: C14.28 Ligand excluded by PLIP C14.7: 4 residues within 4Å: Chain A: F.807, K.1093, Y.1097, I.1101 Ligand excluded by PLIP C14.8: 8 residues within 4Å: Chain A: F.707, F.765, N.1038, V.1039, L.1042, V.1043, F.1046 Ligands: D12.10 Ligand excluded by PLIP C14.21: 5 residues within 4Å: Chain A: I.1064, Y.1067, K.1071 Chain B: V.836, W.840 Ligand excluded by PLIP C14.25: 4 residues within 4Å: Chain B: A.830, V.833, I.837, F.838 Ligand excluded by PLIP C14.26: 5 residues within 4Å: Chain B: F.831, I.877, Y.878, F.881, F.885 Ligand excluded by PLIP C14.27: 8 residues within 4Å: Chain B: N.644, P.645, E.748, R.749, V.866, C.869, A.873, L.948 Ligand excluded by PLIP C14.28: 7 residues within 4Å: Chain A: N.1038, L.1042, I.1045 Chain B: S.848, T.861, F.864 Ligands: C14.6 Ligand excluded by PLIP C14.29: 4 residues within 4Å: Chain A: W.840 Chain B: V.1057, I.1064, K.1093 Ligand excluded by PLIP C14.30: 4 residues within 4Å: Chain B: F.807, K.1093, Y.1097, I.1101 Ligand excluded by PLIP C14.31: 8 residues within 4Å: Chain B: F.707, F.765, N.1038, V.1039, L.1042, V.1043, F.1046 Ligands: D12.33 Ligand excluded by PLIP

10 x D12: DODECANE(Non-covalent)

D12.9: 3 residues within 4Å: Chain A: T.1050, I.1053, V.1057 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.1050, A:I.1053, A:V.1057 D12.10: 4 residues within 4Å: Chain A: H.706, F.707, F.708 Ligands: C14.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.706, A:F.707, A:F.708 D12.11: 1 residues within 4Å: Chain A: V.1100 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1100 D12.12: 4 residues within 4Å: Chain A: I.880, F.881, I.884, V.888 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.880, A:F.881, A:I.884, A:V.888 D12.20: 6 residues within 4Å: Chain A: I.804, S.808, M.876, M.879, S.883, I.953 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.804, A:I.953 D12.32: 3 residues within 4Å: Chain B: T.1050, I.1053, V.1057 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.1050, B:I.1053, B:V.1057 D12.33: 4 residues within 4Å: Chain B: H.706, F.707, F.708 Ligands: C14.31 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:H.706, B:F.707, B:F.708 D12.34: 1 residues within 4Å: Chain B: V.1100 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.1100 D12.35: 3 residues within 4Å: Chain B: I.880, F.881, I.884 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.880, B:F.881, B:I.884 D12.43: 6 residues within 4Å: Chain B: I.804, S.808, M.876, M.879, S.883, I.953 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.804, B:I.953

14 x HP6: HEPTANE(Non-functional Binders)(Non-covalent)

HP6.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.14: 1 residues within 4Å: Chain A: K.863 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.863 HP6.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.17: 1 residues within 4Å: Chain A: C.773 No protein-ligand interaction detected (PLIP) HP6.18: 4 residues within 4Å: Chain A: N.667, F.668, L.790, I.1118 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.667, A:F.668 HP6.19: 3 residues within 4Å: Chain A: N.784, G.786, R.787 No protein-ligand interaction detected (PLIP) HP6.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.37: 2 residues within 4Å: Chain B: E.862, K.863 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.863 HP6.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.40: 1 residues within 4Å: Chain B: C.773 No protein-ligand interaction detected (PLIP) HP6.41: 3 residues within 4Å: Chain B: N.667, F.668, I.1118 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.667, B:F.668 HP6.42: 4 residues within 4Å: Chain B: N.784, G.786, R.787, L.790 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.790

2 x BGI: (2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name)(Non-covalent)

BGI.22: 20 residues within 4Å: Chain A: T.453, M.454, Y.455, E.457, D.500, N.575, K.577, K.578, D.602, A.603, T.605, I.631, Y.654, P.675, A.677, T.744, D.745, Q.756, R.759, W.760 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.455, A:I.631, A:W.760, A:W.760 Hydrogen bonds: A:T.453, A:T.453, A:D.500, A:D.500, A:S.581, A:D.602, A:D.602, A:A.603, A:T.744, A:T.744 Salt bridges: A:K.578, A:R.759 BGI.44: 20 residues within 4Å: Chain B: T.453, M.454, Y.455, E.457, D.500, N.575, K.577, K.578, S.581, D.602, A.603, T.605, Y.654, P.675, A.677, T.744, D.745, Q.756, R.759, W.760 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.455, B:W.760 Hydrogen bonds: B:T.453, B:T.453, B:D.500, B:D.500, B:N.575, B:S.581, B:D.602, B:D.602, B:A.603, B:T.605, B:T.744 Salt bridges: B:K.578, B:R.759

2 x 0V9: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate(Non-covalent)

0V9.23: 22 residues within 4Å: Chain A: L.809, F.813, R.817, L.839, W.840, G.843, I.844, T.846, L.847, F.850, V.1048, V.1055, L.1059, T.1061, I.1087, P.1088 Chain B: V.1048, F.1052, T.1061, G.1062, D.1066 Ligands: 0V9.24 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.809, A:F.813, A:L.839, A:W.840, A:T.846, A:L.847, A:F.850, A:F.850, A:V.1048, A:V.1055, B:V.1048, B:F.1052, B:F.1052, B:F.1052 Salt bridges: A:R.817 0V9.24: 22 residues within 4Å: Chain A: I.1049, F.1052, T.1061, G.1062, D.1066 Chain B: L.809, F.813, R.817, L.839, W.840, G.843, I.844, T.846, L.847, F.850, V.1048, V.1055, L.1059, T.1061, I.1087, P.1088 Ligands: 0V9.23 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.809, B:F.813, B:L.839, B:W.840, B:T.846, B:L.847, B:F.850, B:F.850, B:V.1048, B:V.1055, A:I.1049, A:F.1052, A:F.1052, A:F.1052 Salt bridges: B:R.817

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, Y.N. et al., structure of a membrane-integrated glycosyltransferase with inhibitor. To Be Published

Release Date

2023-05-17

Peptides

Chitin synthase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

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

Chitin synthase 1

Related Entries With Identical Sequence