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SMTL ID : 4jkr.2 (1 other biounit)

Crystal Structure of E. coli RNA Polymerase in complex with ppGpp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

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

Ligands

2 x SR: STRONTIUM ION(Non-functional Binders)

SR.1:	2 residues within 4Å: Chain C: E.813 Chain D: A.459 No protein-ligand interaction detected (PLIP)
SR.4:	2 residues within 4Å: Chain D: D.460, D.464 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.460

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	5 residues within 4Å: Chain D: C.70, L.71, C.72, C.85, C.88 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.70, D:C.72
ZN.3:	5 residues within 4Å: Chain D: C.814, C.888, T.890, 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 G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.5:

12 residues within 4Å:

Chain D: R.362, K.615, V.618, I.619, D.622
Chain E: A.1, R.2, V.3, T.4, D.7, E.41, R.51

14 PLIP interactions:

5 interactions with chain D, 9 interactions with chain E

Hydrogen bonds: D:R.362, D:D.622, E:A.1, E:A.1, E:R.2, E:V.3, E:T.4, E:E.41, E:E.54
Salt bridges: D:K.615, E:R.2, E:R.51
pi-Stacking: D:H.364, D:H.364

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Zuo, Y. et al., The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex. Mol.Cell (2013)

Release Date

2013-05-15

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 RpoD: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

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

Toggle Identical (AB)

DNA-directed RNA polymerase subunit beta

DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor RpoD

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