SMTL ID : 4yfx.1 (1 other biounit)

Escherichia coli RNA polymerase in complex with Myxopyronin B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.84 Å

Oligo State

hetero-oligomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain D: D.460, D.462, D.464 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.460, D:D.462, D:D.464

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain D: C.70, L.71, C.72, G.73, 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: 6 residues within 4Å: Chain D: C.814, R.883, C.888, D.889, 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 4C4: Myxopyronin B(Non-covalent)

4C4.4: 25 residues within 4Å: Chain C: F.1270, G.1271, E.1272, V.1275, W.1276, E.1279, L.1291, S.1322, F.1323, L.1326 Chain D: I.331, K.332, G.333, K.334, L.342, G.344, K.345, V.801, I.1320, A.1323, S.1324, L.1347, K.1348, V.1351, I.1352 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.331, D:K.332, D:L.342, D:V.1351, D:I.1352, C:E.1272, C:L.1326 Hydrogen bonds: D:G.344, D:K.345, D:I.1352, C:E.1279, C:S.1322

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
A

B
B

C
C

D
D

E
E

F
F

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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