SMTL ID : 5d4e.1 (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

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain B: R.30, D.183, D.191, D.193 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.191 MG.4: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: C5P.6 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.5: 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: 5 residues within 4Å: Chain C: E.685, D.686, R.879 Chain D: D.739 Ligands: DPO.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.739 MG.9: 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

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain D: C.1112, C.1194, Q.1195, 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: 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 C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.6: 11 residues within 4Å: Chain C: K.838, K.846 Chain D: R.704, A.705, D.739, D.741, D.743 Chain H: G.14, T.15 Ligands: MG.4, COD.10 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Salt bridges: C:K.838, C:K.846 Hydrogen bonds: D:R.704, D:R.704 Water bridges: D:Q.744, D:Q.744

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.7: 4 residues within 4Å: Chain C: R.879 Chain D: D.739, R.1029 Ligands: MG.8 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:R.879, D:R.1029

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

COD.10: 6 residues within 4Å: Chain C: Q.567, K.838, H.999 Chain H: T.15, A.16 Ligands: C5P.6 2 PLIP interactions: 2 interactions with chain D Water bridges: D:G.742, D:Q.744

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
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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