4xsy.2 | SWISS-MODEL Template Library

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SMTL ID : 4xsy.2 (1 other biounit)

Crystal structure of CBR 9379 bound to Escherichia coli RNA polymerase holoenzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.01 Å

Oligo State

hetero-2-1-1-1-1-mer

Ligands

1 x 42T: 3-{[(2,6-dichlorophenyl)carbamoyl]amino}-N-hydroxy-N'-phenyl-5-(trifluoromethyl)benzenecarboximidamide(Non-covalent)

42T.1:

15 residues within 4Å:

Chain C: D.444, V.550, H.551, P.552, Y.555, R.637, G.640, E.641, S.642
Chain D: K.749, P.750, D.751, I.755, F.773, H.777

12 PLIP interactions:

3 interactions with chain D, 9 interactions with chain C

Hydrophobic interactions: D:K.749, C:P.552, C:P.552, C:Y.555
Hydrogen bonds: D:K.749, C:E.641, C:E.641, C:S.642, C:S.642
Halogen bonds: D:F.773, C:V.550
pi-Stacking: C:H.551

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

Chain D: D.460, D.462, D.464

No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.3:	5 residues within 4Å: Chain D: C.70, C.72, C.85, K.87, C.88 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.70, D:C.72, D:C.85
ZN.4:	4 residues within 4Å: Chain D: C.814, C.888, C.895, C.898 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.814, D:C.888, D:C.895, D:C.898

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Bae, B. et al., CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-07-22

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase sigma factor RpoD: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor RpoD

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