6n61.1 | SWISS-MODEL Template Library

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SMTL ID : 6n61.1

Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Capistruin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

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

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1:

7 residues within 4Å:

Chain C: Q.86, N.139, G.140, T.141, R.758, E.835, K.1051

2 PLIP interactions:

2 interactions with chain C

Hydrogen bonds: C:K.1051, C:K.1051

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

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

4 PLIP interactions:

4 interactions with chain D

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

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 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, T.890, C.895, C.898 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.814, D:C.888, D:C.895

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5:

11 residues within 4Å:

Chain D: Y.511, I.591, Q.594, A.595, L.596, G.597, K.598, K.599, A.600, D.727, S.728

3 PLIP interactions:

3 interactions with chain D

Hydrogen bonds: D:L.596, D:G.597, D:D.727

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Braffman, N.R. et al., Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2019-01-09

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
Capistruin: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

I
I

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

Capistruin

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