SMTL ID : 5d4d.1 (1 other biounit)

Crystal structure of Thermus thermophilus product complex for transcription initiation with NAD and CTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 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: D.183, D.191, L.192, D.193 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.191, B:D.193 MG.4: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: C.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: 4 residues within 4Å: Chain B: E.64, D.168 Chain D: L.839, K.840 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:K.840, H2O.10 MG.8: 3 residues within 4Å: Chain C: E.685 Chain D: D.739 Ligands: CTP.7 No protein-ligand interaction detected (PLIP) 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.2: 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.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 C: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C.6: 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, NAD.9 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.704, D:D.743 Water bridges: D:Q.744, D:Q.744 Salt bridges: C:K.838, C:K.846

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.7: 4 residues within 4Å: Chain C: S.878, R.879 Chain D: R.1029 Ligands: MG.8 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:S.878 Water bridges: C:E.685, C:R.879, C:R.879, D:N.737, D:N.737, D:D.739, D:R.783 Salt bridges: C:R.879, D:R.1029

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.9: 12 residues within 4Å: Chain C: D.396, T.398, Q.567, Q.633, K.838, Y.998, H.999 Chain D: G.742 Chain G: G.14, T.15, A.16 Ligands: C.6 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.567, C:H.999, C:K.1004, D:G.742 Water bridges: C:E.445

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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