6psu.1 | SWISS-MODEL Template Library

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SMTL ID : 6psu.1

Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi2) with TraR and rpsT P2 promoter

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1:	4 residues within 4Å: Chain A: C.36, C.39, C.57, C.60 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.36, A:C.39, A:C.57, A:C.60
ZN.5:	5 residues within 4Å: Chain E: C.70, C.72, K.74, C.85, C.88 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.70, E:C.85, E:C.88
ZN.6:	4 residues within 4Å: Chain E: C.888, V.894, C.895, C.898 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.888, E:C.895, E:C.898

4 x 1N7: CHAPSO(Non-covalent)

1N7.2:	10 residues within 4Å: Chain A: S.9, E.12, Q.13, M.16, T.17, N.20 Chain E: F.935, I.937, L.1243, Q.1244 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:N.20 Hydrophobic interactions: E:F.935, E:L.1243
1N7.3:	7 residues within 4Å: Chain B: D.135 Chain D: Q.725, Y.726, E.962, Q.965, I.966, A.969 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.726, D:Y.726, D:E.962, D:Q.965, D:A.969
1N7.7:	7 residues within 4Å: Chain D: Q.1264 Chain E: L.255, D.256 Chain G: I.514, D.516, F.525 Ligands: 1N7.8 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:F.525 Hydrogen bonds: E:D.256
1N7.8:	9 residues within 4Å: Chain D: S.508 Chain E: R.259 Chain G: I.508, T.512, P.513, I.514, G.515, L.522 Ligands: 1N7.7 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:I.508, G:I.514 Hydrogen bonds: E:R.259

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

4 residues within 4Å:

Chain E: R.425, D.460, D.462, D.464

4 PLIP interactions:

4 interactions with chain E

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

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

Protein TraR: A
DNA-directed RNA polymerase subunit alpha: BCJ
DNA-directed RNA polymerase subunit beta: D
DNA-directed RNA polymerase subunit beta': E
DNA-directed RNA polymerase subunit omega: F
RNA polymerase sigma factor RpoD: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
G

C
H

J
M

D
I

E
J

F
K

G
L

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Protein TraR

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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