6psr.1 | SWISS-MODEL Template Library

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SMTL ID : 6psr.1

Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1) with TraR and rpsT P2 promoter

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-1-1-1-mer

Ligands

4 x 1N7: CHAPSO(Non-covalent)

1N7.1:	8 residues within 4Å: Chain A: E.72, D.135 Chain C: Q.725, Y.726, E.962, Q.965, I.966, A.969 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.726, C:E.962, C:I.966 Hydrogen bonds: C:E.962, C:Q.965
1N7.5:	8 residues within 4Å: Chain D: D.256, R.259 Chain F: I.508, T.512, P.513, I.514, L.522 Ligands: 1N7.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.259
1N7.6:	9 residues within 4Å: Chain D: F.935, I.937, L.1243, Q.1244 Chain H: S.9, Q.13, M.16, T.17, N.20 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain D Hydrophobic interactions: H:Q.13, H:Q.13, H:M.16, H:N.20, D:I.937
1N7.7:	8 residues within 4Å: Chain D: L.255, D.256 Chain F: I.514, G.515, D.516, F.525, E.527 Ligands: 1N7.5 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:L.255, F:I.514, F:F.525, F:F.525 Hydrogen bonds: D:D.256

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

3 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:	6 residues within 4Å: Chain D: C.814, R.883, C.888, T.890, 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
ZN.8:	4 residues within 4Å: Chain H: C.36, C.39, C.57, C.60 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.36, H:C.39, H:C.57, H:C.60

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Chen, J. et al., Stepwise Promoter Melting by Bacterial RNA Polymerase. Mol.Cell (2020)

Release Date

2020-03-25

Peptides

DNA-directed RNA polymerase subunit alpha: ABG
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
Protein TraR: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

G
M

C
I

D
J

E
K

F
L

H
N

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

Protein TraR

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