SMTL ID : 9v4m.1

Crystal structure of the T.thermophilus transcription initiation complex bound to Ap4G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

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

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.51, V.170 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:V.170 MG.2: 3 residues within 4Å: Chain B: E.154, D.168 Chain D: K.840 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:D.168, D:K.840 MG.7: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: 01.3 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.739, D:D.739, D:D.741, D:D.743, H2O.2 MG.8: 2 residues within 4Å: Chain D: N.737, D.739 No protein-ligand interaction detected (PLIP)

1 x 01: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate

01.3: 19 residues within 4Å: Chain C: Q.393, F.394, H.406, R.409, E.445, Q.567, K.838, K.846, H.999 Chain D: R.704, A.705, P.706, D.739, D.741, G.742, D.743 Chain G: C.15, G.16 Ligands: MG.7 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:F.394, C:R.409, C:E.445, C:E.445, C:E.445, C:Q.567, D:R.704, D:R.704, D:A.705, D:A.705, D:D.741 Salt bridges: C:K.838, C:K.838, C:K.838, C:K.846, C:H.999, C:H.999 Water bridges: D:D.739

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 4 residues within 4Å: Chain C: G.951, L.952, Q.969 Chain D: Y.1015 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.951, C:Q.969 TRS.9: 4 residues within 4Å: Chain A: R.30, G.31 Chain B: R.42 Chain D: A.854 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.30, B:R.42

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 7 residues within 4Å: Chain D: C.1112, T.1114, R.1189, C.1194, Q.1195, 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: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, W. et al., Molecular basis for noncanonical transcription initiation from Np4A alarmones. Nat.Chem.Biol. (2025)

Release Date

2025-10-22

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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