SMTL ID : 5x21.1

Crystal structure of Thermus thermophilus transcription initiation complex with GpA and pseudouridimycin (PUM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.32 Å

Oligo State

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

Ligands

1 x G- A: RNA (5'-R(*GP*A)-3')(Non-covalent)

G-A.1: 14 residues within 4Å: Chain C: Q.567, K.838, K.846, H.999, K.1004 Chain D: R.704, D.739, D.741, D.743 Chain G: T.15, C.16, G.17 Ligands: MG.7, PUM.10 Protein-ligand interaction information (PLIP) not available

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 6 residues within 4Å: Chain A: T.51, V.170, F.171, S.172, R.175, D.202 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:V.170 MG.3: 4 residues within 4Å: Chain C: S.387, R.388, S.389, S.392 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.389 MG.4: 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.7: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: G-A.1 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.741, D:D.743, D:D.743 MG.8: 3 residues within 4Å: Chain F: A.312, G.316, W.319 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:A.312, F:G.316, F:W.319 MG.9: 2 residues within 4Å: Chain H: G.19, G.20 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 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.6: 6 residues within 4Å: Chain D: C.58, C.60, G.61, K.62, 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 PUM: (1S)-1,4-anhydro-5-[(N-carbamimidoylglycyl-N~2~-hydroxy-L-glutaminyl)amino]-5-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol(Non-covalent)

PUM.10: 12 residues within 4Å: Chain C: E.445, K.846 Chain D: R.704, P.706, N.737, T.1084, Q.1235, M.1238, F.1241 Chain G: A.14, T.15 Ligands: G-A.1 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.1241 Hydrogen bonds: D:R.704, D:R.704, D:N.737, D:Q.1235, D:Q.1235, C:E.445, C:K.846 Salt bridges: C:E.445

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maffioli, S.I. et al., Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase. Cell (2017)

Release Date

2017-07-05

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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