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SMTL ID : 4kn4.2 (1 other biounit)

X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.97 Å

Oligo State

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

Ligands

1 x 1RL: Benzoxazinorifamycin-2b(Non-covalent)

1RL.1:

20 residues within 4Å:

Chain C: R.143, S.509, Q.510, L.511, S.512, Q.513, F.514, D.516, H.526, R.529, S.531, L.533, G.534, R.540, P.564, N.568, I.572, R.687
Chain F: D.513, D.514

9 PLIP interactions:

9 interactions with chain C

Hydrophobic interactions: C:F.514, C:F.514, C:D.516, C:L.533
Hydrogen bonds: C:R.143, C:F.514, C:F.514, C:F.514, C:S.531

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	4 residues within 4Å: Chain D: C.70, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.70, D:C.72, D:C.85, D:C.88
ZN.3:	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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

3 residues within 4Å:

Chain C: K.1073
Chain D: D.462, D.464

1 PLIP interactions:

1 interactions with chain D

Metal complexes: D:D.462

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Molodtsov, V. et al., X-ray Crystal Structures of the Escherichia coli RNA Polymerase in Complex with Benzoxazinorifamycins. J.Med.Chem. (2013)

Release Date

2013-05-22

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
F

B
G

C
H

D
I

E
J

F
Y

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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