SMTL ID : 6n8e.1

Crystal structure of holo-ObiF1, a five domain nonribosomal peptide synthetase from Burkholderia diffusa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.1: 18 residues within 4Å: Chain A: A.38, I.39, I.41, G.42, L.45, Y.52, H.164, L.242, A.316, N.317, V.318, R.352, E.354, R.357, R.358, I.363, S.1036, F.1054 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.45, A:I.363 Hydrogen bonds: A:A.38, A:A.38, A:E.354, A:E.354 Salt bridges: A:R.358

1 x KFG: dimethyl hydrogen phosphate(Non-covalent)

KFG.2: 8 residues within 4Å: Chain A: G.841, A.842, L.844, G.868, T.869, R.870, N.1355, L.1357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.870 Salt bridges: A:R.870

1 x KFJ: 4-(4-nitrophenyl)-L-threonine(Non-covalent)

KFJ.3: 17 residues within 4Å: Chain A: H.677, F.681, D.682, A.683, W.686, G.725, Q.726, I.727, C.754, G.756, G.757, M.782, G.784, I.785, T.786, I.790, N.791 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.681, A:A.683, A:I.790 Hydrogen bonds: A:D.682, A:G.784, A:T.786, A:T.786

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

CL.4: 3 residues within 4Å: Chain A: L.854, V.857, R.1382 Ligand excluded by PLIP

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

PO4.5: 7 residues within 4Å: Chain A: H.43, Q.44, R.136, I.137, D.138, L.139, S.140 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.44, A:D.138, A:L.139 Salt bridges: A:H.43, A:R.136 PO4.6: 1 residues within 4Å: Chain A: R.591 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.591

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kreitler, D.F. et al., The structural basis of N-acyl-alpha-amino-beta-lactone formation catalyzed by a nonribosomal peptide synthetase. Nat Commun (2019)

Release Date

2019-07-24

Peptides

holo-ObiF1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

holo-ObiF1