6byu.1 | SWISS-MODEL Template Library

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SMTL ID : 6byu.1 (1 other biounit)

X-ray crystal structure of Escherichia coli RNA polymerase (RpoB-H526Y) and ppApp complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

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

Ligands

1 x ECJ: (5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate(Covalent)

ECJ.1:

8 residues within 4Å:

Chain C: K.1242, Q.1268
Chain D: R.346, R.352, N.424, R.425, A.426, Q.465

7 PLIP interactions:

4 interactions with chain D, 3 interactions with chain C

Hydrogen bonds: D:N.424, C:Q.1268
Salt bridges: D:R.346, D:R.352, D:R.352, C:K.1242, C:K.1242

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

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

5 PLIP interactions:

5 interactions with chain D

Metal complexes: D:D.460, D:D.462, D:D.462, D:D.464, D:D.464

2 x ZN: ZINC ION(Non-covalent)

ZN.3:	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.4:	5 residues within 4Å: Chain D: C.814, 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

Bruhn-Olszewska, B. et al., Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro. Biochim. Biophys. Acta (2018)

Release Date

2018-01-17

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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