SMTL ID : 5x22.2 (1 other biounit)

Crystal structure of Thermus thermophilus transcription initiation complex with GpA and CMPcPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.35 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.5, 2TM.9 Protein-ligand interaction information (PLIP) not available

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: D.183, D.191, L.192, D.193 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.183, B:D.191, B:D.193 MG.5: 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.6: 2 residues within 4Å: Chain D: D.739 Ligands: 2TM.9 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: D.168 Chain D: K.840 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.840 MG.8: 3 residues within 4Å: Chain D: W.897, E.898, I.900 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:W.897, D:E.898, D:I.900 MG.10: 4 residues within 4Å: Chain F: A.312, E.313, G.316, W.319 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:A.312, F:G.316, F:W.319

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 5 residues within 4Å: Chain D: C.58, C.60, 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 2TM: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine(Non-covalent)

2TM.9: 11 residues within 4Å: Chain C: R.557, R.879 Chain D: R.704, P.706, N.737, Q.1235, M.1238, T.1240 Chain G: G.14 Ligands: G-A.1, MG.6 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:K.846, D:R.704, D:R.704, D:N.737, D:Q.1235, D:Q.1235, D:M.1238, D:T.1240 Salt bridges: C:R.557, C:R.879

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
K

B
L

C
M

D
N

E
O

F
P

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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