7khb.1 | SWISS-MODEL Template Library

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SMTL ID : 7khb.1

Escherichia coli RNA polymerase and rrnBP1 promoter open complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x 1N7: CHAPSO(Non-covalent)

1N7.1:	7 residues within 4Å: Chain A: D.135 Chain C: Q.725, Y.726, Q.965, I.966, A.969, R.976 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.726, C:Q.965, C:I.966, C:A.969 Hydrogen bonds: C:Y.726
1N7.2:	9 residues within 4Å: Chain C: Q.46, S.398, A.399, V.400, R.452, E.458, E.461, E.583, Y.584 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:E.458, C:Y.584 Hydrogen bonds: C:S.398, C:A.399, C:V.400, C:E.583 Salt bridges: C:E.583

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

3 residues within 4Å:

Chain D: D.460, 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:	6 residues within 4Å: Chain D: C.70, C.72, G.73, K.74, 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.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

Shin, Y. et al., Structural basis of ribosomal RNA transcription regulation. Nat Commun (2021)

Release Date

2020-10-28

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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