SMTL ID : 5oa4.1

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72I mutant in complex with 4-methoxycyclopeptin (1)

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: TRS.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.134, A:D.136, A:H.211 NI.5: 4 residues within 4Å: Chain B: H.134, D.136, H.211 Ligands: TRS.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.134, B:D.136, B:H.211

2 x 58D: (3S)-3-(4-methoxybenzyl)-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione(Non-covalent)

58D.2: 15 residues within 4Å: Chain A: N.70, I.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: TRS.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.72, A:L.73, A:L.79, A:T.227 Hydrogen bonds: A:N.70, A:M.137 Water bridges: A:R.138, A:F.139, A:S.140 pi-Stacking: A:H.134 58D.6: 15 residues within 4Å: Chain A: I.273 Chain B: N.70, I.72, L.73, L.79, M.118, M.122, Q.131, P.132, H.134, D.136, M.137, F.139, T.227 Ligands: TRS.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.72, B:L.73, B:L.79, B:T.227 Hydrogen bonds: B:N.70, B:M.137 Water bridges: B:R.138, B:F.139, B:S.140 pi-Stacking: B:H.134

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 9 residues within 4Å: Chain A: M.122, Q.131, H.134, D.136, N.157, L.159, H.211 Ligands: NI.1, 58D.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.131, A:Q.131 TRS.7: 9 residues within 4Å: Chain B: M.122, Q.131, H.134, D.136, N.157, L.159, H.211 Ligands: NI.5, 58D.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.131, B:Q.131

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

CL.4: 4 residues within 4Å: Chain A: T.172, G.213, R.223, L.225 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: T.172, G.213, R.223, L.225 Ligand excluded by PLIP

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

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