SMTL ID : 4zxi.1

Crystal Structure of holo-AB3403 a four domain nonribosomal peptide synthetase bound to AMP and Glycine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.1: 13 residues within 4Å: Chain A: G.25, I.29, Y.39, H.147, T.300, F.335, S.336, V.339, R.346, N.351, P.352, H.1007, S.1008 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.29, A:F.335, A:V.339, A:P.352 Hydrogen bonds: A:Y.39, A:T.300, A:N.351, A:N.351, A:S.1008 Salt bridges: A:R.346

1 x GLY: GLYCINE(Non-covalent)

GLY.2: 12 residues within 4Å: Chain A: F.671, D.672, I.673, G.741, G.764, P.765, T.766, V.770, W.771, K.954 Ligands: AMP.3, MG.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.765, A:T.766 Salt bridges: A:K.954

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 17 residues within 4Å: Chain A: T.627, S.628, G.741, E.742, A.743, N.761, V.762, Y.763, G.764, P.765, L.785, D.851, H.863, R.866, K.954 Ligands: GLY.2, MG.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.628, A:S.628, A:S.628, A:G.741, A:V.762, A:G.764, A:D.851, A:K.954 Salt bridges: A:R.866, A:K.954 pi-Stacking: A:Y.763, A:Y.763

1 x XP4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

XP4.4: 15 residues within 4Å: Chain A: H.2, L.53, P.57, I.58, L.61, F.96, W.127, C.131, Y.139, F.143, I.145, L.159, V.162, F.166, L.387 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.53, A:P.57, A:L.61, A:L.61, A:W.127, A:F.143, A:F.143, A:I.145, A:V.162, A:F.166, A:F.166, A:F.166, A:L.387

1 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 3 residues within 4Å: Chain A: G.1, H.2, M.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.2

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: T.627, T.766 Ligands: GLY.2, AMP.3 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Metal complexes: GLY.2, A:T.766

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drake, E.J. et al., Structures of two distinct conformations of holo-non-ribosomal peptide synthetases. Nature (2016)

Release Date

2015-12-30

Peptides

Tyrocidine synthetase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrocidine synthetase 3

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