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SMTL ID : 6x50.1

Mfd-bound E.coli RNA polymerase elongation complex - V state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1:

19 residues within 4Å:

Chain A: F.597, F.599, E.600, T.601, T.602, Q.605, V.630, G.631, F.632, G.633, K.634, T.635, D.729, E.730, R.783, G.874, D.876, R.905
Ligands: MG.2

18 PLIP interactions:

18 interactions with chain A

Hydrogen bonds: A:E.600, A:T.602, A:Q.605, A:G.631, A:F.632, A:G.633, A:K.634, A:T.635, A:T.635, A:T.635, A:E.730, A:R.783, A:D.876
Salt bridges: A:K.634, A:K.634, A:R.905, A:R.905
pi-Stacking: A:F.599

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2:	5 residues within 4Å: Chain A: T.635, H.665, D.729, L.754 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.635, A:D.729, A:D.729
MG.3:	4 residues within 4Å: Chain E: D.460, D.462, D.464 Chain G: A.20 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.460, E:D.460, E:D.462, E:D.464

2 x ZN: ZINC ION(Non-covalent)

ZN.4:	4 residues within 4Å: Chain E: C.70, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.70, E:C.72, E:C.85, E:C.88
ZN.5:	5 residues within 4Å: Chain E: C.814, R.883, C.888, C.895, C.898 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.814, E:C.888, E:C.895, E:C.898

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Kang, J.Y. et al., Structural basis for transcription complex disruption by the Mfd translocase. Elife (2021)

Release Date

2021-02-03

Peptides

Transcription-repair-coupling factor: A
DNA-directed RNA polymerase subunit alpha: BC
DNA-directed RNA polymerase subunit beta: D
DNA-directed RNA polymerase subunit beta': E
DNA-directed RNA polymerase subunit omega: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

C
H

D
I

E
J

F
K

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Transcription-repair-coupling factor

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

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