SMTL ID : 6mfy.1

Crystal structure of a 5-domain construct of LgrA in the substrate donation state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.1: 14 residues within 4Å: Chain A: D.730, S.731, H.910, G.915, T.1015, Y.1017, M.1018, V.1043, T.1044, D.1045, V.1060, M.1121, M.1122, Q.1123 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.1017, A:T.1044 Hydrogen bonds: A:S.731, A:S.731, A:T.1015, A:M.1018, A:D.1045, A:M.1122

10 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: A.54, Y.55, N.73, H.75, G.84, D.110 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.55, A:Y.55, A:N.73, A:G.84 Water bridges: A:A.54 Salt bridges: A:H.75 PO4.3: 6 residues within 4Å: Chain A: T.353, S.354, P.485, T.486, E.487 Ligands: PO4.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.354, A:T.486, A:E.487 PO4.4: 7 residues within 4Å: Chain A: Y.812, S.1132, M.1134, H.1135, H.1136, L.1151, R.1153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.1136 Water bridges: A:K.918, A:R.1153 Salt bridges: A:R.1153 PO4.5: 2 residues within 4Å: Chain A: H.246, S.332 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.246 PO4.6: 6 residues within 4Å: Chain A: T.353, S.354, S.356, T.357, K.361 Ligands: PO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.353, A:T.353, A:T.353, A:S.354, A:T.357, A:T.357 Salt bridges: A:K.361 PO4.7: 5 residues within 4Å: Chain A: T.1371, P.1514, T.1515, E.1516, Y.1598 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.1515, A:T.1515, A:T.1515 PO4.8: 7 residues within 4Å: Chain A: D.398, Y.441, G.465, G.484, P.485, T.486, I.490 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.398, A:D.398, A:G.484, A:G.484 Water bridges: A:G.465 PO4.9: 5 residues within 4Å: Chain A: N.1036, D.1070, E.1072, R.1551, H.1552 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.1036, A:E.1072 Water bridges: A:E.1072, A:R.1551 Salt bridges: A:R.1551 PO4.10: 3 residues within 4Å: Chain A: N.815, N.1133, H.1135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.815, A:N.1133 Salt bridges: A:H.1135 PO4.11: 5 residues within 4Å: Chain A: S.805, I.806, F.988, D.989, I.1141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.806 Water bridges: A:F.988, A:D.989

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reimer, J.M. et al., Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility. Science (2019)

Release Date

2019-11-20

Peptides

Linear gramicidin synthase subunit A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Linear gramicidin synthase subunit A

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