- PDB-4cc6: Fragment-Based Discovery of 6 Azaindazoles As Inhibitors of Bacte... -
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Basic information
Entry
Database: PDB / ID: 4cc6
Title
Fragment-Based Discovery of 6 Azaindazoles As Inhibitors of Bacterial DNA Ligase
Components
DNA LIGASE
Keywords
LIGASE / LIGA / ANTIBIOTIC DESIGN
Function / homology
Function and homology information
DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA replication / DNA binding / metal ion binding / cytosol Similarity search - Function
Dna Ligase; domain 1 - #70 / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation ...Dna Ligase; domain 1 - #70 / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain / Ligase N family / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / DNA ligase/mRNA capping enzyme / Helix hairpin bin / RuvA domain 2-like / Helix-hairpin-helix domain / BRCA1 C Terminus (BRCT) domain / D-amino Acid Aminotransferase; Chain A, domain 1 / breast cancer carboxy-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Dna Ligase; domain 1 / Helix Hairpins / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 2.01→42.51 Å / Cor.coef. Fo:Fc: 0.8537 / Cor.coef. Fo:Fc free: 0.8194 / SU R Cruickshank DPI: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.212 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2958
1122
5.3 %
RANDOM
Rwork
0.2288
-
-
-
obs
0.2323
21180
95.01 %
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Displacement parameters
Biso mean: 33.77 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.1427 Å2
0 Å2
-1.3973 Å2
2-
-
-6.4138 Å2
0 Å2
3-
-
-
4.2711 Å2
Refine analyze
Luzzati coordinate error obs: 0.292 Å
Refinement step
Cycle: LAST / Resolution: 2.01→42.51 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2488
0
28
101
2617
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.011
2574
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.12
3490
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
923
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
88
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
371
HARMONIC
5
X-RAY DIFFRACTION
t_it
2574
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
6.72
X-RAY DIFFRACTION
t_other_torsion
17.19
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
321
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
3157
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.01→2.11 Å / Total num. of bins used: 11
Rfactor
Num. reflection
% reflection
Rfree
0.2635
126
5.05 %
Rwork
0.192
2370
-
all
0.1956
2496
-
obs
-
-
95.01 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.5567
-0.3226
0.2314
1.093
1.1944
0.685
-0.0347
-0.0566
0.0381
-0.0658
-0.0019
-0.0321
-0.0181
0.0368
0.0365
-0.1695
-0.0065
-0.0158
0.1453
0.0035
-0.0247
10.1734
18.0007
38.2815
2
0.9922
0.2936
-0.5515
1.2265
-0.1283
1.2483
0.0062
0.0581
-0.0227
-0.0552
-0.0111
-0.064
0.0002
0.0393
0.0049
-0.2287
0.0213
-0.0054
0.0956
-0.0033
-0.0598
26.1344
18.408
15.1665
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|2 - A|60 }
2
X-RAY DIFFRACTION
2
{ A|61 - A|309 }
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