5D4D: Crystal structure of Thermus thermophilus product complex for transcription initiation with NAD and CTP

PDB ID: 5D4DDownload
MMDB ID: 140872
PDB Deposition Date: 2015/8/7
Updated in MMDB: 2023/10
Experimental Method:
x-ray diffraction
Resolution: 3  Å
Source Organism:
Thermus thermophilus HB8▼
Similar Structures:
Biological Unit for 5D4D: octameric; determined by author and by software (PISA)
Molecular Components in 5D4D
Label Count Molecule
Proteins (6 molecules)
2
DNA-directed RNA Polymerase Subunit Alpha
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Beta
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Beta'
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Omega
Molecule annotation
1
RNA Polymerase Sigma Factor Siga
Molecule annotation
Nucleotides(2 molecules)
1
DNA (5'-d(*cp*c*tp*gp*cp*ap*tp*cp*cp*gp*tp*gp*ap*gp*tp*ap*gp*ap*g)-3')
Molecule annotation
1
DNA (27-mer)
Molecule annotation
Chemicals and Non-standard biopolymers (10 molecules)
1
5
MAGNESIUM IONMAGNESIUM ION
2
2
ZINC IONZINC ION
3
1
CYTIDINE-5'-MONOPHOSPHATECYTIDINE-5'-MONOPHOSPHATE
4
1
CYTIDINE-5'-TRIPHOSPHATECYTIDINE-5'-TRIPHOSPHATE
5
1
NICOTINAMIDE-ADENINE-DINUCLEOTIDENICOTINAMIDE-ADENINE-DINUCLEOTIDE
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303