SMTL ID : 4oir.1

Crystal structure of Thermus thermophilus RNA polymerase transcription initiation complex soaked with GE23077 and rifamycin SV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

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

Ligands

1 x 2RA- DSN- DVA- R2T- 2TL- 0QZ- FGL: GE23077(Non-covalent)

2RA-DSN-DVA-R2T-2TL-0QZ-FGL.1: 14 residues within 4Å: Chain C: P.444, E.445, G.446, R.557, L.559, M.560, N.563, M.564, Q.567, K.838, K.846 Chain D: D.741 Ligands: MG.6, MB8.9 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.445, C:E.445, C:E.445, C:E.445, C:E.445, C:E.445, C:E.445, C:G.446, C:R.557, C:R.557, C:N.563, C:Q.567, C:K.838, C:K.846, D:D.741

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: E.154, D.168 Chain D: K.840 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.840 MG.6: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: 2RA-DSN-DVA-R2T-2TL-0QZ-FGL.1 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.739, D:D.741, D:D.743, H2O.3, H2O.3 MG.7: 3 residues within 4Å: Chain D: W.897, E.898, I.900 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:I.900 MG.8: 4 residues within 4Å: Chain F: A.312, E.313, G.316, W.319 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:G.316, F:W.319

1 x RFV: rifamycin SV(Non-covalent)

RFV.3: 17 residues within 4Å: Chain C: Q.390, L.391, S.392, Q.393, F.394, D.396, R.405, H.406, R.409, S.411, L.413, R.420, P.444, N.448, I.452, Q.633 Chain F: D.343 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: C:L.391, C:Q.393, C:F.394, C:L.413, C:L.413, C:P.444, C:I.452, F:D.343 Hydrogen bonds: C:Q.393, C:F.394, C:F.394, C:S.411, C:S.411, C:R.420, C:R.420, C:N.448, F:D.343, F:D.343

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain D: C.1112, C.1194, T.1196, C.1201, C.1204 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1112, D:C.1194, D:C.1201, D:C.1204 ZN.5: 4 residues within 4Å: Chain D: C.58, C.60, C.73, C.76 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.58, D:C.60, D:C.73, D:C.76

1 x MB8: (2Z)-2-methylbut-2-enoic acid(Non-functional Binders)

MB8.9: 2 residues within 4Å: Chain G: G.17 Ligands: 2RA-DSN-DVA-R2T-2TL-0QZ-FGL.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides. Elife (2014)

Release Date

2014-05-07

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
DNA directed RNA polymerase sigma factor A: 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

DNA directed RNA polymerase sigma factor A

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