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SMTL ID : 5uah.1 (1 other biounit)

Escherichia coli RNA polymerase and Rifampin complex, RpoB D516V mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.10 Å

Oligo State

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

Ligands

1 x RFP: RIFAMPICIN(Non-covalent)

RFP.1:

15 residues within 4Å:

Chain C: R.143, S.509, Q.510, L.511, S.512, Q.513, F.514, V.516, R.529, S.531, L.533, R.540, P.564, I.572, R.687

12 PLIP interactions:

12 interactions with chain C

Hydrophobic interactions: C:L.511, C:F.514, C:V.516, C:L.533, C:P.564
Hydrogen bonds: C:R.143, C:Q.513, C:F.514, C:F.514, C:S.531, C:S.531, C:R.540

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2:	3 residues within 4Å: Chain C: E.813 Chain D: A.459, D.460 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Metal complexes: D:D.460, C:E.813, C:E.813
MG.3:	2 residues within 4Å: Chain D: D.462, D.464 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.462, D:D.462, D:D.464, D:D.464

2 x ZN: ZINC ION(Non-covalent)

ZN.4:	5 residues within 4Å: Chain D: C.70, C.72, C.85, K.87, 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.5:	6 residues within 4Å: Chain D: C.814, R.883, C.888, D.889, 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

Molodtsov, V. et al., Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis. Mol. Microbiol. (2017)

Release Date

2017-01-11

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
F

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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