SMTL ID : 6pst.1

Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1.5b) with TraR and mutant rpsT P2 promoter

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-1-1-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.36, C.39, C.57, C.60 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.36, A:C.39, A:C.57, A:C.60 ZN.5: 4 residues within 4Å: Chain H: C.70, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.70, H:C.72, H:C.85, H:C.88 ZN.6: 6 residues within 4Å: Chain H: C.814, C.888, D.889, T.890, C.895, C.898 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.814, H:C.888, H:C.895, H:C.898

4 x 1N7: CHAPSO(Non-covalent)

1N7.2: 10 residues within 4Å: Chain A: S.9, E.12, Q.13, M.16, T.17, N.20 Chain H: F.935, I.937, L.1243, Q.1244 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain A Hydrophobic interactions: H:I.937, A:Q.13, A:M.16 1N7.3: 9 residues within 4Å: Chain E: E.72, D.135, E.136 Chain G: Q.725, Y.726, E.962, Q.965, I.966, A.969 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:Y.726, G:E.962, G:I.966, G:A.969 Hydrogen bonds: G:Q.965 1N7.7: 9 residues within 4Å: Chain G: Q.1264 Chain H: L.255, D.256 Chain J: I.514, D.517, L.522, F.525, I.526 Ligands: 1N7.8 6 PLIP interactions: 2 interactions with chain H, 4 interactions with chain J Hydrophobic interactions: H:L.255, J:I.514, J:I.514, J:L.522, J:F.525 Hydrogen bonds: H:D.256 1N7.8: 8 residues within 4Å: Chain H: L.255, R.259 Chain J: I.508, T.512, P.513, I.514, L.522 Ligands: 1N7.7 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:R.259

1 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J. et al., Stepwise Promoter Melting by Bacterial RNA Polymerase. Mol.Cell (2020)

Release Date

2020-03-25

Peptides

Protein TraR: A
DNA-directed RNA polymerase subunit alpha: DEF
DNA-directed RNA polymerase subunit beta: G
DNA-directed RNA polymerase subunit beta': H
DNA-directed RNA polymerase subunit omega: I
RNA polymerase sigma factor RpoD: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

D
M

E
G

F
H

G
I

H
J

I
K

J
L

Protein TraR

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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