SMTL ID : 6fbv.1

Single particle cryo em structure of Mycobacterium tuberculosis RNA polymerase in complex with Fidaxomicin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.52 Å

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain D: C.891, C.968, C.975, C.978 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.891, D:C.968, D:C.975, D:C.978 ZN.2: 4 residues within 4Å: Chain D: C.60, C.62, C.75, C.78 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.60, D:C.62, D:C.75, D:C.78

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain D: D.535, D.537, D.539 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.535, D:D.535, D:D.537, D:D.539, H2O.1

1 x FI8: Fidaxomicin(Non-covalent)

FI8.4: 20 residues within 4Å: Chain C: M.1051, I.1052, Q.1054, D.1094, T.1096, V.1097, K.1101, E.1119, S.1120 Chain D: D.57, R.84, K.86, R.89, E.323, L.324, V.328, R.412, Q.415 Chain F: L.423, D.424 20 PLIP interactions: 8 interactions with chain C, 11 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: C:I.1052, C:V.1097, C:E.1119, D:V.328, F:L.423 Hydrogen bonds: C:T.1096, C:T.1096, C:T.1096, C:K.1101, C:K.1101, D:D.57, D:K.86, D:R.89, D:R.89, D:E.323, D:R.412 Salt bridges: D:R.84, D:R.89, D:R.412 pi-Cation interactions: D:R.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, W. et al., Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Mol. Cell (2018)

Release Date

2018-02-28

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 SigA: 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 SigA

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