SMTL ID : 6p4u.2 (1 other biounit)

The structure of condensation and adenylation domains of teixobactin-producing nonribosomal peptide synthetase Txo1 serine module in complex with Mg and AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: G.733, E.734, A.735, N.755, L.756, Y.757, G.758, P.759, T.760, I.782, D.849, Y.861, R.864 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.733, A:L.756, A:G.758, A:T.760, A:D.849, A:Y.861, A:R.864 Water bridges: A:D.662, A:D.662, A:S.732, A:N.755 pi-Stacking: A:Y.757, A:Y.757 AMP.25: 14 residues within 4Å: Chain B: G.733, E.734, A.735, N.755, L.756, Y.757, G.758, P.759, T.760, I.782, D.849, Y.861, R.864 Ligands: MG.26 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.733, B:L.756, B:G.758, B:T.760, B:T.760, B:D.849, B:R.864 Water bridges: B:D.662, B:D.662, B:S.732, B:N.755 pi-Stacking: B:Y.757, B:Y.757

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.758, V.764, D.765 Ligands: AMP.1 6 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:G.758, A:V.764, H2O.1, H2O.1, H2O.2, AMP.1 MG.26: 4 residues within 4Å: Chain B: G.758, V.764, D.765 Ligands: AMP.25 6 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:G.758, B:V.764, H2O.7, H2O.7, H2O.8, AMP.25

34 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: D.513, R.515, L.611, R.818 Ligands: SO4.4 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: M.628, Y.820, L.821, G.822 Ligands: SO4.3 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.496, Q.497, R.500 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: R.496, R.500, P.595, A.596, Q.597 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: R.414, A.443, E.444, R.447 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: H.609, H.610 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: S.568, G.585, E.586 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: Q.642 Ligands: SO4.18 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: E.718, G.719, V.720, Q.721 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: E.630, R.843 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: S.620, R.864, D.866 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: G.186, E.187, R.188 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: R.457, E.458, H.459 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain A: P.548, A.549 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: G.619, S.620, R.830 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain A: L.639, A.673, V.674 Ligands: SO4.10 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain A: W.179, R.188 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain B: D.513, R.515, L.611, R.818 Ligands: SO4.28 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain B: M.628, Y.820, L.821, G.822 Ligands: SO4.27 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: R.496, Q.497, R.500 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain B: R.496, R.500, P.595, A.596, Q.597 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain B: R.414, A.443, E.444, R.447 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain B: H.609, H.610 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain B: S.568, G.585, E.586 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain B: Q.642 Ligands: SO4.42 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain B: E.718, G.719, V.720, Q.721 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain B: E.630, R.843 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain B: S.620, R.864, D.866 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain B: G.186, E.187, R.188 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain B: R.457, E.458, H.459 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain B: P.548, A.549 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain B: G.619, S.620, R.830 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain B: L.639, A.673, V.674 Ligands: SO4.34 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain B: W.179, R.188 Ligand excluded by PLIP

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 3 residues within 4Å: Chain A: R.823, P.824, E.825 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain B: R.823, P.824, E.825 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.21: 5 residues within 4Å: Chain A: T.462, E.467, R.601, V.606, Q.607 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.601 Hydrogen bonds: A:E.467 ACT.45: 5 residues within 4Å: Chain B: T.462, E.467, R.601, V.606, Q.607 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.601 Hydrogen bonds: B:E.467

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 1 residues within 4Å: Chain A: P.840 No protein-ligand interaction detected (PLIP) GOL.23: 5 residues within 4Å: Chain A: R.522, K.656, P.658, Q.684, Q.686 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.522, A:R.522, A:K.656, A:Q.686 Water bridges: A:E.521, A:R.522 GOL.46: 1 residues within 4Å: Chain B: P.840 No protein-ligand interaction detected (PLIP) GOL.47: 5 residues within 4Å: Chain B: R.522, K.656, P.658, Q.684, Q.686 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.522, B:R.522, B:K.656, B:Q.686 Water bridges: B:E.521, B:E.521

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.24: 3 residues within 4Å: Chain A: T.657, F.661, V.707 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.705, A:V.707 FMT.48: 3 residues within 4Å: Chain B: T.657, F.661, V.707 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.707

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., Structures of teixobactin-producing nonribosomal peptide synthetase condensation and adenylation domains. Curr Res Struct Biol (2020)

Release Date

2019-06-12

Peptides

Txo1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Txo1

Related Entries With Identical Sequence