7mkn.1 | SWISS-MODEL Template Library

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SMTL ID : 7mkn.1

Escherichia coli RNA polymerase and RapA elongation complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1:

4 residues within 4Å:

Chain D: D.447, D.449, D.451
Chain H: A.11

4 PLIP interactions:

4 interactions with chain D

Metal complexes: D:D.449, D:D.449, D:D.451, D:D.451

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	6 residues within 4Å: Chain D: C.57, C.59, G.60, K.61, C.72, C.75 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.57, D:C.59, D:C.72, D:C.75
ZN.3:	7 residues within 4Å: Chain D: C.801, R.870, C.875, D.876, T.877, C.882, C.885 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.801, D:C.875, D:C.882, D:C.885

1 x 2TM: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine(Non-covalent)

2TM.4:

9 residues within 4Å:

Chain C: S.1103, R.1104
Chain D: R.412, P.414, N.445, D.447, R.718
Chain H: A.11
Chain I: G.14

5 PLIP interactions:

2 interactions with chain C, 3 interactions with chain D

Hydrogen bonds: C:S.1103, C:R.1104, D:R.412, D:D.447
Salt bridges: D:R.718

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Qayyum, M.Z. et al., Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli. J.Biol.Chem. (2021)

Release Date

2021-06-02

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-associated protein RapA: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
L

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-associated protein RapA

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