SMTL ID : 6fm4.1

The crystal structure of S. aureus Gyrase complex with ID-130 and DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: Y.523, K.524, T.526, Q.529 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.523 MN.2: 5 residues within 4Å: Chain A: E.27, D.100, D.102 Chain C: G.7, G.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.27, A:D.100, A:D.100 MN.5: 4 residues within 4Å: Chain B: E.27, D.100 Chain D: G.7, G.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.27, B:D.100

2 x 5UA: 5'-O-CARBOXY-2'-DEOXYADENOSINE(Non-functional Binders)(Non-covalent)

5UA.3: 2 residues within 4Å: Chain C: G.1 Chain D: C.18 No protein-ligand interaction detected (PLIP) 5UA.6: 3 residues within 4Å: Chain B: R.60 Chain C: T.19 Chain D: G.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.60, B:R.60

1 x DU5: ~{N}-[3-(4-isoquinolin-1-ylpiperazin-1-yl)propyl]benzamide(Non-covalent)

DU5.4: 12 residues within 4Å: Chain A: A.269, G.273, M.276, D.284, M.322 Chain B: M.276, D.284, M.322 Chain C: G.9, C.10 Chain D: G.9, C.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.284 Hydrophobic interactions: A:D.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Magaro, G. et al., Virtual Screening Approach and Investigation of Structure-Activity Relationships To Discover Novel Bacterial Topoisomerase Inhibitors Targeting Gram-Positive and Gram-Negative Pathogens. J.Med.Chem. (2019)

Release Date

2019-07-10

Peptides

DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A

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