SMTL ID : 7l7b.1

Clostridioides difficile RNAP with fidaxomicin

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain D: C.790, C.864, K.865, T.866, C.871, C.874 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.790, D:C.864, D:C.871, D:C.874 ZN.2: 7 residues within 4Å: Chain D: C.60, C.62, G.63, K.64, C.75, R.77, 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.449, D.451, D.453 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.449, D:D.449, D:D.451, D:D.453, H2O.1

1 x FI8: Fidaxomicin(Non-covalent)

FI8.4: 29 residues within 4Å: Chain C: L.1099, V.1100, T.1101, Q.1102, D.1142, D.1143, V.1144, V.1145, V.1148, R.1149, E.1167, S.1168, V.1171 Chain D: K.84, S.85, K.86, R.89, D.237, L.238, P.240, V.242, S.252, K.314, M.319, R.326, Q.329 Chain F: L.285, E.286, A.306 22 PLIP interactions: 11 interactions with chain D, 8 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: D:L.238, D:P.240, C:V.1100, C:V.1144, C:V.1145, C:V.1148, C:E.1167, F:L.285, F:E.286 Hydrogen bonds: D:K.84, D:K.86, D:D.237, D:R.326, D:R.326, D:Q.329, C:Q.1102, C:V.1144, C:R.1149 Salt bridges: D:K.86, D:R.89, D:R.326 Water bridges: F:H.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, X. et al., Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Nature (2022)

Release Date

2022-02-02

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