SMTL ID : 6vvt.1

Crystal structure of a Mycobacterium smegmatis transcription initiation complex with Rifampicin-resistant RNA polymerase and antibiotic Sorangicin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

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

Ligands

1 x SRN: SORANGICIN A(Non-covalent)

SRN.1: 14 residues within 4Å: Chain D: V.167, Q.426, S.428, Q.429, F.430, D.432, T.441, H.442, R.445, L.447, P.480, N.484, I.488, R.604 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:V.167, D:Q.426, D:Q.429, D:F.430, D:D.432, D:R.445, D:P.480, D:I.488 Hydrogen bonds: D:Q.429, D:F.430, D:T.441, D:R.445

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain D: N.1102 Chain F: R.59, D.63 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.59

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain E: C.890, R.962, C.967, C.974, C.977 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.890, E:C.967, E:C.974, E:C.977 ZN.4: 6 residues within 4Å: Chain E: C.60, Y.61, C.62, G.63, C.75, C.78 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.60, E:C.62, E:C.75, E:C.78

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 7 residues within 4Å: Chain E: D.882, V.883, T.971, G.972, R.1160, Q.1161, R.1164 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.1160, E:R.1164 SO4.6: 4 residues within 4Å: Chain E: R.894, G.895, K.960, R.1129 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.895 Salt bridges: E:K.960, E:R.1129 SO4.7: 5 residues within 4Å: Chain E: R.886, E.887, H.888, I.990, R.1267 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.886, E:H.888 Salt bridges: E:R.1267 SO4.8: 2 residues within 4Å: Chain E: R.421, R.427 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.421, E:R.427 SO4.9: 5 residues within 4Å: Chain A: R.57 Chain D: R.1139 Chain E: N.22, W.23, Y.25 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Salt bridges: D:R.1139, A:R.57 SO4.10: 5 residues within 4Å: Chain E: R.389 Chain G: M.253, A.254, F.255, L.256 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G Salt bridges: E:R.389 Hydrogen bonds: G:L.256 SO4.11: 3 residues within 4Å: Chain G: R.190, R.228, H.232 2 PLIP interactions: 2 interactions with chain G Salt bridges: G:R.190, G:H.232 SO4.12: 1 residues within 4Å: Chain G: K.210 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:K.210 SO4.13: 3 residues within 4Å: Chain G: S.406, R.408, E.409 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.406, G:E.409 Salt bridges: G:R.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lilic, M. et al., The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-10-21

Peptides

RNA polymerase-binding protein RbpA: A
DNA-directed RNA polymerase subunit alpha: BC
DNA-directed RNA polymerase subunit beta: D
DNA-directed RNA polymerase subunit beta': E
DNA-directed RNA polymerase subunit omega: F
RNA polymerase sigma factor SigA: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
A

C
B

D
C

E
D

F
E

G
F

RNA polymerase-binding protein RbpA

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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