8sy6.1 | SWISS-MODEL Template Library

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SMTL ID : 8sy6.1

E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-mer

Ligands

1 x A- U- C- G- A- G- A- G- G: RNA oligomer(Non-covalent)

A-U-C-G-A-G-A-G-G.1:

27 residues within 4Å:

Chain B: C.20, C.21, T.22, C.23, T.24, C.25, G.26, A.27, T.28
Chain D: Q.510, Q.513, R.540, N.568, I.572, R.687, Q.688, K.1065, K.1073, H.1237
Chain E: R.425, A.426, P.427, D.462, D.464
Ligands: DGP.2, MG.5, UTP.6

1 PLIP interactions:

1 interactions with chain D

Hydrogen bonds: D:R.542

1 x DGP: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

DGP.2:

6 residues within 4Å:

Chain B: T.28
Chain E: L.255, R.259, A.261, T.262
Ligands: A-U-C-G-A-G-A-G-G.1

1 PLIP interactions:

1 interactions with chain E

Hydrogen bonds: E:R.259

2 x ZN: ZINC ION(Non-covalent)

ZN.3:	4 residues within 4Å: Chain E: C.814, 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
ZN.4:	5 residues within 4Å: Chain E: C.72, C.85, E.86, K.87, C.88 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:C.72

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5:

5 residues within 4Å:

Chain E: D.460, D.462, D.464
Ligands: A-U-C-G-A-G-A-G-G.1, UTP.6

5 PLIP interactions:

5 interactions with chain E

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

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.6:

17 residues within 4Å:

Chain B: G.19
Chain D: R.678, M.681, D.814, K.1073, R.1106
Chain E: R.425, P.427, N.458, D.460, D.462, D.464, M.932, F.935, H.936
Ligands: A-U-C-G-A-G-A-G-G.1, MG.5

9 PLIP interactions:

5 interactions with chain E, 4 interactions with chain D

Hydrogen bonds: E:R.425, E:R.425, E:N.458, E:D.462
Salt bridges: E:H.936, D:R.678, D:K.1073, D:K.1073, D:R.1106

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Oh, J. et al., A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. Nat Commun (2023)

Release Date

2023-12-27

Peptides

DNA-directed RNA polymerase subunit alpha: CG
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:

C
G

G
A

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

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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