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SMTL ID : 9gdd.1

RNAP-TopoI complex on bubble scaffold - two-bubble configuration

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.460, D.462, D.464
Chain H: G.14

5 PLIP interactions:

5 interactions with chain D

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

5 x ZN: ZINC ION(Non-covalent)

ZN.2:	4 residues within 4Å: Chain D: C.70, C.72, 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.3:	5 residues within 4Å: Chain D: C.814, R.883, C.888, 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.4:	4 residues within 4Å: Chain F: C.630, C.633, C.650, C.661 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.630, F:C.633, F:C.650, F:C.661
ZN.5:	4 residues within 4Å: Chain F: C.693, C.696, C.714, C.720 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.693, F:C.696, F:C.714, F:C.720
ZN.6:	4 residues within 4Å: Chain F: C.742, C.745, C.762, C.767 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.742, F:C.745, F:C.762, F:C.767

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Vidmar, V. et al., DNA topoisomerase I acts as supercoiling sensor for transcription elongation in E. coli. To Be Published

Release Date

2025-11-05

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
DNA topoisomerase 1: 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

DNA topoisomerase 1

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

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