SMTL ID : 6sul.2 (1 other biounit)

Amicoumacin kinase AmiN in complex with AMP-PNP, Mg2+ and Ami

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.219, D.222 Ligands: MG.2, ANP.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.219, A:D.219, H2O.2, H2O.2 MG.2: 5 residues within 4Å: Chain A: H.204, N.207, D.219 Ligands: MG.1, ANP.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.219, H2O.9 MG.7: 4 residues within 4Å: Chain B: D.219, D.222 Ligands: MG.8, ANP.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.219, B:D.219, H2O.17, H2O.19 MG.8: 5 residues within 4Å: Chain B: H.204, N.207, D.219 Ligands: MG.7, ANP.13 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.219, H2O.21

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

CL.3: 4 residues within 4Å: Chain A: R.26, I.29, H.30, F.31 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: G.78, L.79, S.80, R.136, K.214 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: K.163, L.164, R.165 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: E.274 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: N.192, Q.193 Ligand excluded by PLIP

2 x UAM: Amicoumacin A(Non-covalent)

UAM.5: 17 residues within 4Å: Chain A: E.36, E.159, Q.161, D.202, H.204, H.205, G.206, D.222, N.238, W.241, Y.242, R.286, L.289, I.290, L.293 Chain B: A.309 Ligands: ANP.6 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.204, A:N.238, A:W.241, A:W.241, A:Y.242, A:L.289, A:L.293, B:A.309 Hydrogen bonds: A:E.36, A:Q.161, A:H.204, A:G.206, A:D.222, A:R.286 Water bridges: A:R.59, A:R.59, A:H.205, A:D.222, A:R.286, A:R.286 Salt bridges: A:H.204 pi-Stacking: A:H.204, A:H.205, A:Y.242 UAM.12: 18 residues within 4Å: Chain A: D.305, A.309 Chain B: E.36, E.159, Q.161, D.202, H.204, H.205, G.206, D.222, N.238, W.241, Y.242, R.286, L.289, I.290, L.293 Ligands: ANP.13 23 PLIP interactions: 1 interactions with chain A, 22 interactions with chain B Hydrophobic interactions: A:A.309, B:H.204, B:N.238, B:W.241, B:W.241, B:Y.242, B:L.289, B:L.293 Hydrogen bonds: B:E.36, B:Q.161, B:H.204, B:D.222, B:R.286 Water bridges: B:R.59, B:R.59, B:K.116, B:H.205, B:R.286, B:R.286 Salt bridges: B:H.204 pi-Stacking: B:H.204, B:H.205, B:Y.242

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.6: 22 residues within 4Å: Chain A: I.32, A.35, E.36, N.37, V.39, I.50, K.52, A.82, E.110, K.111, A.112, K.116, D.202, H.204, G.206, N.207, H.209, F.218, D.219 Ligands: MG.1, MG.2, UAM.5 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.36, A:N.37, A:N.37, A:K.52, A:E.110, A:A.112, A:K.116, A:K.116, A:N.207, A:D.219, A:D.219 Water bridges: A:A.35, A:A.35, A:K.116, A:K.116, A:G.206, A:N.207 Salt bridges: A:K.52 pi-Stacking: A:F.218, A:F.218 ANP.13: 22 residues within 4Å: Chain B: I.32, A.35, E.36, N.37, V.39, I.50, K.52, A.82, E.110, K.111, A.112, K.116, D.202, H.204, G.206, N.207, H.209, F.218, D.219 Ligands: MG.7, MG.8, UAM.12 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:E.36, B:N.37, B:N.37, B:K.52, B:E.110, B:A.112, B:K.116, B:K.116, B:N.207, B:D.219 Water bridges: B:A.35, B:A.35, B:K.116, B:G.206, B:N.207, B:D.219, B:D.219, B:D.219, B:D.221 Salt bridges: B:K.52 pi-Stacking: B:F.218, B:F.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Terekhov, S.S. et al., A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding. Sci Adv (2020)

Release Date

2020-07-22

Peptides

Phosphotransferase enzyme family protein, amicoumacin kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Phosphotransferase enzyme family protein, amicoumacin kinase

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