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SMTL ID : 5ipm.1

SigmaS-transcription initiation complex with 4-nt nascent RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

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

Ligands

1 x GTP- A- G- U: nascent RNA 4-mer(Non-covalent)

GTP-A-G-U.1:

24 residues within 4Å:

Chain C: Q.513, R.529, P.564, R.687, Q.688, K.1065, K.1073, H.1237
Chain D: R.425, A.426, P.427, N.458, D.460, D.462, G.463, D.464, T.786, M.932
Chain H: A.10, C.11, T.12, C.13, G.14
Ligands: MG.4

3 PLIP interactions:

3 interactions with chain C

Hydrogen bonds: C:Q.688
Salt bridges: C:R.529, C:R.687

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	5 residues within 4Å: Chain D: C.70, C.72, K.74, 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

5 residues within 4Å:

Chain D: D.460, D.462, D.464
Ligands: GTP-A-G-U.1, GTP-A-G-U.1

4 PLIP interactions:

4 interactions with chain D

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Liu, B. et al., Structures of E. coli sigma S-transcription initiation complexes provide new insights into polymerase mechanism. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-03-30

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 sigma factor RpoS: 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

RNA polymerase sigma factor RpoS

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