4yfk.2 | SWISS-MODEL Template Library

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

Escherichia coli RNA polymerase in complex with squaramide compound 8.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.57 Å

Oligo State

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

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1:	5 residues within 4Å: Chain C: E.813 Chain D: C.454, N.458, A.459, D.460 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.813
MG.2:	3 residues within 4Å: Chain D: D.460, D.462, D.464 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.462, D:D.462, D:D.464, D:D.464

2 x ZN: ZINC ION(Non-covalent)

ZN.3:	4 residues within 4Å: Chain D: C.70, C.72, C.85, C.88 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.70, D:C.72, D:C.85
ZN.4:	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 4C6: 3,5-dimethyl-N-{2-[4-(4-methylbenzyl)piperidin-1-yl]-3,4-dioxocyclobut-1-en-1-yl}-1,2-oxazole-4-sulfonamide(Non-covalent)

4C6.5:

18 residues within 4Å:

Chain C: F.1270, G.1271, E.1272, L.1291, L.1326, I.1330
Chain D: I.331, K.332, L.342, L.343, G.344, K.345, I.1320, A.1323, T.1328, L.1332, V.1351, I.1352

9 PLIP interactions:

3 interactions with chain C, 6 interactions with chain D

Hydrophobic interactions: C:L.1291, C:L.1326, C:I.1330, D:I.331, D:I.1320, D:A.1323, D:T.1328, D:L.1332, D:V.1351

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Molodtsov, V. et al., X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein. J.Med.Chem. (2015)

Release Date

2015-03-11

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

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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