SMTL ID : 6mfw.1

Crystal structure of a 4-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 JQG: (2~{R})-~{N}-[3-[2-[[(2~{S})-2-formamido-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]-3,3-dimethyl-2-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-butanamide(Covalent)

JQG.1: 25 residues within 4Å: Chain A: D.730, S.731, Y.750, V.810, Y.812, H.910, L.913, D.914, G.915, K.918, T.1015, Y.1017, M.1018, V.1043, T.1044, D.1045, V.1060, L.1086, L.1090, M.1121, M.1122, Q.1123, H.1136, K.1143, E.1149 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.1017, A:T.1044 Hydrogen bonds: A:S.731, A:S.731, A:Y.812, A:H.910, A:G.915, A:T.1015, A:D.1045, A:D.1045, A:M.1122, A:Q.1123, A:E.1149 Water bridges: A:Y.1017

1 x FON: N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid(Non-covalent)

FON.2: 19 residues within 4Å: Chain A: S.52, Y.55, G.56, Y.57, I.58, L.59, N.73, H.75, R.85, H.103, I.105, D.106, E.107, H.108, V.109, D.110, F.168, K.169, A.170 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.58, A:F.168 Hydrogen bonds: A:Y.55, A:Y.57, A:L.59, A:L.59, A:N.73, A:D.110, A:K.169 Water bridges: A:D.106, A:T.111

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.3: 21 residues within 4Å: Chain A: T.353, S.354, G.464, G.465, D.466, V.467, N.481, G.482, Y.483, G.484, P.485, T.486, I.506, T.568, D.570, F.582, R.585, N.672, K.674 Ligands: VAL.4, MG.6 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.354, A:S.354, A:S.354, A:G.465, A:N.481, A:N.481, A:G.484, A:T.486, A:T.486, A:T.486, A:D.570, A:D.570, A:R.585, A:K.674 Water bridges: A:T.353, A:K.361 pi-Stacking: A:Y.483

1 x VAL: VALINE(Non-covalent)

VAL.4: 11 residues within 4Å: Chain A: D.398, G.399, L.402, Y.441, G.464, G.465, G.484, I.490, M.491, K.674 Ligands: APC.3 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:I.490 Hydrogen bonds: A:D.398, A:Y.441, A:Y.441 Salt bridges: A:K.674

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

PO4.5: 4 residues within 4Å: Chain A: L.78, Q.117, E.118, E.119 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.117, A:Q.117

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.6: 1 residues within 4Å: Ligands: APC.3 No protein-ligand interaction detected (PLIP)

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