SMTL ID : 6eoz.1

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72K mutant in complex with cyclopeptin (1b)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.134, D.136, H.211 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.134, A:D.136, A:H.211, H2O.1 NI.4: 4 residues within 4Å: Chain B: H.134, D.136, H.211 Ligands: AKG.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.134, B:D.136, B:H.211, H2O.13

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 13 residues within 4Å: Chain A: L.73, M.122, Q.131, H.134, D.136, L.159, T.172, H.211, G.213, R.223, L.225 Ligands: NI.1, 58K.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.159 Hydrogen bonds: A:Q.131 Water bridges: A:Q.131 Salt bridges: A:H.134, A:R.223 AKG.5: 13 residues within 4Å: Chain B: L.73, M.122, Q.131, H.134, D.136, L.159, T.172, H.211, G.213, R.223, L.225 Ligands: NI.4, 58K.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.159 Hydrogen bonds: B:Q.131 Water bridges: B:Q.131 Salt bridges: B:H.134, B:R.223

2 x 58K: cyclopeptin(Non-covalent)

58K.3: 15 residues within 4Å: Chain A: N.70, K.72, L.73, L.79, M.118, M.122, Q.131, P.132, H.134, D.136, M.137, F.139, T.227 Chain B: I.273 Ligands: AKG.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.73, A:L.79, A:P.132, A:H.134, A:F.139 Hydrogen bonds: A:N.70, A:M.137 Water bridges: A:R.138, A:F.139 pi-Stacking: A:H.134 58K.6: 15 residues within 4Å: Chain A: I.273 Chain B: N.70, K.72, L.73, L.79, M.118, M.122, Q.131, P.132, H.134, D.136, M.137, F.139, T.227 Ligands: AKG.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.73, B:L.79, B:P.132, B:H.134, B:F.139 Hydrogen bonds: B:N.70, B:M.137 Water bridges: B:R.138, B:F.139 pi-Stacking: B:H.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mader, S.L. et al., Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ. Nat Commun (2018)

Release Date

2018-04-04

Peptides

Iron/alpha-ketoglutarate-dependent dioxygenase asqJ: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Iron/alpha-ketoglutarate-dependent dioxygenase asqJ