SMTL ID : 5d4e.2 (1 other biounit)

Crystal structure of Thermus thermophilus product complex for transcription initiation with 3'-dephosphate-CoA and CTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.08 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 B: D.168 Chain D: K.840 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.840 MG.4: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: C5P.5 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.741, D:D.743 MG.7: 3 residues within 4Å: Chain C: E.685 Chain D: D.739 Ligands: DPO.6 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.739, H2O.2 MG.8: 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.2: 6 residues within 4Å: Chain D: C.1112, R.1189, 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.3: 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 C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.5: 10 residues within 4Å: Chain C: K.838, K.846 Chain D: R.704, A.705, D.739, D.741, D.743 Chain G: G.14 Ligands: MG.4, COD.9 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Salt bridges: C:K.838, C:K.846 Hydrogen bonds: D:R.704

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.6: 4 residues within 4Å: Chain C: R.879 Chain D: D.739, R.1029 Ligands: MG.7 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Water bridges: C:R.557, C:R.879 Salt bridges: C:R.879, D:R.1029

1 x COD: DEPHOSPHO COENZYME A(Non-covalent)

COD.9: 9 residues within 4Å: Chain C: Q.567, K.838, Y.998, H.999 Chain D: G.742 Chain G: G.14, T.15, A.16 Ligands: C5P.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.567, C:Y.998

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bird, J.G. et al., The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA. Nature (2016)

Release Date

2016-07-06

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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