6QX2 Isomerase date Mar 06, 2019
title 3.4a Structure Of Benzoisoxazole 3 With S.Aureus Dna Gyrase
authors B.D.Bax
compound source
Molecule: Dna Gyrase Subunit B,Dna Gyrase Subunit B
Chain: B, S, b, s
Ec: 5.99.1.3,5.99.1.3
Engineered: Yes
Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyrb, Gyrb, Sav0005
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Gyrase Subunit A
Chain: A, C, L, R, T, a, c, j, l, r, t
Ec: 5.99.1.3
Engineered: Yes
Mutation: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyra, Sa0006
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Gyrase Subunit B,Dna Gyrase Subunit B
Chain: D, U, m
Ec: 5.99.1.3,5.99.1.3
Engineered: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyrb, Gyrb, Sar0005
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Gpapgpcpgptpapcpgpgpcpcpgptpapcpgpcptp
Chain: E, F, N, O, W, e, n, v, w
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630

Molecule: Dna Gyrase Subunit B,Dna Gyrase Subunit B
Chain: K
Ec: 5.99.1.3,5.99.1.3
Engineered: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyrb, Sa0005, Gyrb, Sausa300_0005
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Gyrase Subunit A
Chain: J
Ec: 5.99.1.3
Engineered: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyra, Sa0006
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Gyrase Subunit B,Dna Gyrase Subunit B
Chain: M
Ec: 5.99.1.3,5.99.1.3
Engineered: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyrb, Sa0005, Gyrb, Sausa300_0005
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Gpapgpcpgptpapcpgpgpcpcpgptpapcpgpcptp
Chain: V, o
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630

Molecule: Dna Gyrase Subunit B,Dna Gyrase Subunit B
Chain: d
Ec: 5.99.1.3,5.99.1.3
Engineered: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyrb, Sa0005, Gyrb, Sar0005
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Gpapgpcpgptpapcpgpgpcpcpgptpapcpgpcptp
Chain: f
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630

Molecule: Dna Gyrase Subunit B,Dna Gyrase Subunit B
Chain: k
Ec: 5.99.1.3,5.99.1.3
Engineered: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyrb, Sa0005, Gyrb, Sar0005
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Gyrase Subunit B,Dna Gyrase Subunit B
Chain: u
Ec: 5.99.1.3,5.99.1.3
Engineered: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyrb, Sa0005, Gyrb, Sausa300_0005
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.176 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
187.640 410.120 93.940 90.00 120.22 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand JK8 enzyme Isomerase E.C.5.99.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
S, K, d, u, k, M, m, s, B, D, b, U


r, a, T, j, C, L, t, A, J, l, c, R


Primary referenceStructure-guided design of antibacterials that allosterically inhibit DNA gyrase., Thalji RK, Raha K, Andreotti D, Checchia A, Cui H, Meneghelli G, Profeta R, Tonelli F, Tommasi S, Bakshi T, Donovan BT, Howells A, Jain S, Nixon C, Quinque G, McCloskey L, Bax BD, Neu M, Chan PF, Stavenger RA, Bioorg Med Chem Lett. 2019 Mar 22. pii: S0960-894X(19)30168-4. doi:, 10.1016/j.bmcl.2019.03.029. PMID:30962087
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1395 Kb) [Save to disk]
  • Biological Unit Coordinates (6qx2.pdb1.gz) 244 Kb
  • Biological Unit Coordinates (6qx2.pdb2.gz) 243 Kb
  • Biological Unit Coordinates (6qx2.pdb3.gz) 243 Kb
  • Biological Unit Coordinates (6qx2.pdb4.gz) 239 Kb
  • Biological Unit Coordinates (6qx2.pdb5.gz) 242 Kb
  • Biological Unit Coordinates (6qx2.pdb6.gz) 244 Kb
  • LPC: Ligand-Protein Contacts for 6QX2
  • CSU: Contacts of Structural Units for 6QX2
  • Structure Factors (3068 Kb)
  • Retrieve 6QX2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6QX2 from S2C, [Save to disk]
  • View 6QX2 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6QX2
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6qx2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6qx2_N] [6qx2_O] [6qx2_r] [6qx2_U] [6qx2_C] [6qx2_e] [6qx2_V] [6qx2_u] [6qx2_v] [6qx2_d] [6qx2_R] [6qx2_A] [6qx2_B] [6qx2_M] [6qx2_b] [6qx2_F] [6qx2_f] [6qx2_m] [6qx2_T] [6qx2_l] [6qx2_S] [6qx2_w] [6qx2_J] [6qx2_n] [6qx2_s] [6qx2_W] [6qx2_E] [6qx2_j] [6qx2_a] [6qx2_t] [6qx2_K] [6qx2_L] [6qx2_D] [6qx2_o] [6qx2_c] [6qx2_k]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6QX2
  • Community annotation for 6QX2 at PDBWiki (http://pdbwiki.org)

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