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SMTL ID : 4kmu.1 (1 other biounit)

X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.85 Å

Oligo State

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

Ligands

1 x RFP: RIFAMPICIN(Non-covalent)

RFP.1:

16 residues within 4Å:

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

15 PLIP interactions:

15 interactions with chain C

Hydrophobic interactions: C:Q.513, C:F.514, C:D.516, C:L.533, C:L.533, C:I.572
Hydrogen bonds: C:Q.513, C:Q.513, C:F.514, C:F.514, C:S.531, C:S.531, C:R.540, C:N.568
Salt bridges: C:R.143

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	6 residues within 4Å: Chain D: C.70, C.72, G.73, K.74, C.85, C.88 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.70, D:C.72, D:C.85
ZN.3:	4 residues within 4Å: Chain D: C.814, C.888, C.895, C.898 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.814, D:C.888, D:C.898

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

4 residues within 4Å:

Chain D: R.425, D.460, D.462, D.464

3 PLIP interactions:

3 interactions with chain D

Metal complexes: D:D.462, D:D.464, D:D.464

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
A

B
B

C
C

D
D

E
E

F
X

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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