SMTL ID : 3jz0.1

LinB complexed with clindamycin and AMPCPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.60, E.62 Ligands: MG.2, APC.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.60, A:E.62, H2O.2 MG.2: 6 residues within 4Å: Chain A: D.60, E.62, E.109 Ligands: MG.1, APC.4, CLY.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.60, A:E.62, A:E.109, H2O.8 MG.3: 1 residues within 4Å: Chain A: D.83 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.83, H2O.13, H2O.13, H2O.13, H2O.13 MG.6: 4 residues within 4Å: Chain B: D.60, E.62 Ligands: MG.7, APC.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.60, B:E.62, H2O.15 MG.7: 6 residues within 4Å: Chain B: D.60, E.62, E.109 Ligands: MG.6, APC.8, CLY.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.60, B:E.62, B:E.109, H2O.19

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

APC.4: 15 residues within 4Å: Chain A: Y.47, G.48, S.49, K.52, S.59, D.60, E.62, L.217, N.218, K.221 Chain B: R.185, R.190 Ligands: MG.1, MG.2, CLY.5 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.49, A:S.49, A:K.52, A:K.52, A:S.59, A:D.60, A:L.217 Water bridges: A:G.48, A:K.52, A:Y.58, A:R.107, A:R.107, A:K.221, B:R.190, B:R.190 Salt bridges: A:K.221, B:R.185, B:R.190 APC.8: 15 residues within 4Å: Chain A: R.185, R.190 Chain B: Y.47, G.48, S.49, K.52, S.59, D.60, E.62, L.217, N.218, K.221 Ligands: MG.6, MG.7, CLY.9 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.49, B:S.49, B:K.52, B:K.52, B:S.59, B:D.60, B:L.217 Water bridges: B:G.48, B:K.52, B:Y.58, B:R.107, B:R.107, B:N.218, B:K.221, A:R.190, A:R.190 Salt bridges: B:K.221, A:R.185, A:R.190

2 x CLY: CLINDAMYCIN(Non-covalent)

CLY.5: 12 residues within 4Å: Chain A: Y.47, E.62, Y.64, Y.95, E.109, H.111, F.124, S.127, I.130, M.136 Ligands: MG.2, APC.4 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.47, A:Y.47, A:Y.64, A:Y.95, A:F.124, A:I.130 Hydrogen bonds: A:Y.47 Water bridges: A:D.60, A:E.109, B:R.190 CLY.9: 10 residues within 4Å: Chain B: Y.47, E.62, Y.64, Y.95, E.109, F.124, S.127, I.130 Ligands: MG.7, APC.8 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.47, B:Y.47, B:Y.64, B:Y.95, B:F.124, B:F.124, B:I.130 Hydrogen bonds: B:Y.47 Water bridges: B:Y.47, B:Y.47, B:D.60, B:E.109, A:R.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morar, M. et al., Structure and mechanism of the lincosamide antibiotic adenylyltransferase LinB. Structure (2009)

Release Date

2009-11-03

Peptides

Lincosamide nucleotidyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lincosamide nucleotidyltransferase

Related Entries With Identical Sequence