SMTL ID : 7en1.1

Pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module-after-condensation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.1: 21 residues within 4Å: Chain A: V.110, A.113, Y.114, L.116, E.122, N.368, L.391, L.427, L.430, R.431, R.434, V.445, T.474, P.475, Q.476, V.477, D.1384, S.1385, L.1386, Y.1409 Ligands: J9F.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.427, A:L.430, A:R.431, A:R.434, A:Q.476 Hydrogen bonds: A:E.122, A:N.368, A:P.475, A:Q.476, A:S.1385, A:L.1386 Salt bridges: A:R.431 PNS.6: 26 residues within 4Å: Chain B: D.45, S.46, I.47, M.50, Y.114, L.236, D.240, V.241, E.242, T.343, S.345, S.346, V.369, P.370, L.371, F.372, T.389, L.392, L.415, H.416, I.419, F.446, A.447, S.448, N.449 Ligands: SAL.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.369, B:F.372, B:L.415 Hydrogen bonds: B:S.46, B:D.240, B:V.241, B:T.343, B:S.345, B:S.345, B:S.346, B:S.346, B:P.370, B:F.372, B:S.448, B:S.448, B:N.449

1 x J9F: (4S)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid(Non-covalent)

J9F.2: 22 residues within 4Å: Chain A: V.110, Y.114, C.129, H.130, A.131, L.236, V.241, P.370, T.389, L.391, V.445, A.447, M.470, L.471, S.472, Q.473, T.474, V.477, D.480, Q.482, Y.484 Ligands: PNS.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.131, A:L.236, A:V.241

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 1 residues within 4Å: Ligands: AMP.4 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: AMP.4 MG.8: 6 residues within 4Å: Chain B: T.697, A.841, T.842, E.843, R.953 Ligands: AMP.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:T.842, B:E.843, AMP.9, AMP.9

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 19 residues within 4Å: Chain A: S.813, G.814, D.815, W.816, V.817, V.837, L.838, G.839, G.840, A.841, T.842, Y.865, T.925, D.927, F.939, R.942, K.1325 Ligands: MG.3, CYS.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.814, A:L.838, A:G.840, A:Y.865, A:D.927, A:D.927, A:R.942 Salt bridges: A:K.1325 pi-Stacking: A:Y.865 AMP.9: 23 residues within 4Å: Chain B: S.813, G.814, D.815, W.816, V.817, V.837, L.838, G.839, G.840, A.841, T.842, E.843, Y.865, I.894, T.925, D.927, F.939, R.942, Q.946, K.948, R.953 Ligands: MG.8, CYS.10 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:G.814, B:L.838, B:G.840, B:T.842, B:T.842, B:Y.865, B:D.927, B:D.927, B:R.942, C.10 Salt bridges: B:K.948, B:R.953 pi-Stacking: B:F.939

2 x CYS: CYSTEINE(Non-covalent)

CYS.5: 12 residues within 4Å: Chain A: F.741, D.742, L.743, S.813, G.814, G.840, A.841, T.842, I.846, W.847, K.1325 Ligands: AMP.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.742, A:K.1325 CYS.10: 13 residues within 4Å: Chain B: F.741, D.742, L.743, S.813, G.814, G.839, G.840, A.841, T.842, G.845, I.846, W.847 Ligands: AMP.9 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: B:T.842, C.10, C.10, C.10, C.10

1 x SAL: 2-HYDROXYBENZOIC ACID(Non-covalent)

SAL.7: 16 residues within 4Å: Chain B: Y.114, C.129, H.130, A.131, L.236, V.241, A.447, M.470, L.471, S.472, Q.473, T.474, D.480, Q.482, Y.484 Ligands: PNS.6 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.131, B:L.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Catalytic trajectory of a dimeric nonribosomal peptide synthetase subunit with an inserted epimerase domain. Nat Commun (2022)

Release Date

2021-12-22

Peptides

Dihydroaeruginoic acid synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroaeruginoic acid synthetase

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