Research workbench
Crystal structure of thermus thermophilus product complex for transcription initiation with NAD and CTP
Analyse Crystal structure of thermus thermophilus product complex for transcription… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D4D
- Type
- protein + DNA
- Length
- 6,992 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- Q9Z9H6, Q8RQE9, Q8RQE8, Q8RQE7, Q72L95
- Ligands
- C, CTP, NAD, A, MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 12 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 22% helix, 40% strand | Q9Z9H6 |
| B, L | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 22% helix, 43% strand | Q9Z9H6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1108 | 30% helix, 27% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1485 | 37% helix, 25% strand | Q8RQE8 |
| E, O | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 51% helix, 11% strand | Q8RQE7 |
| F | RNA polymerase sigma factor siga | protein | 346 | 69% helix, 1% strand | Q72L95 |
| G, R | DNA (5'- D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') | dna | 16 | — | — |
| H, S | DNA (27-mer) | dna | 21 | — | — |
| K | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 19% helix, 42% strand | Q9Z9H6 |
| M | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1091 | 29% helix, 26% strand | Q8RQE9 |
| N | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1483 | 36% helix, 24% strand | Q8RQE8 |
| P | RNA polymerase sigma factor siga | protein | 316 | 68% helix, 2% strand | Q72L95 |
Ligands and binding sites
- C · Cytidine-5'-monophosphate · ligand · 2 copies · chains C, D, G, M, N, R
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains C, D, M, N
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains C, D, G
- A · Adenosine-5'-monophosphate · ligand · chains M, N, R
- MG · Magnesium ion · metal · 10 copies · chains B, D, C, F, L, N, M, P
- ZN · Zinc ion · metal · 4 copies · chains D, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.87 | 0.89 | 141 | empty |
| 2 | 1055 | 0.86 | 0.87 | 96 | MG |
| 3 | 1168 | 0.86 | 0.87 | 129 | MG |
| 4 | 1122 | 0.84 | 0.85 | 97 | empty |
| 5 | 448 | 0.84 | 0.91 | 60 | empty |
Interfaces
37 interfaces between chains.
- M–N · 8976 Ų buried · 131 hydrogen bonds · protein-protein
- C–D · 8973 Ų buried · 136 hydrogen bonds · protein-protein
- D–F · 4065 Ų buried · 53 hydrogen bonds · protein-protein
- N–P · 4044 Ų buried · 53 hydrogen bonds · protein-protein
- C–F · 2559 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5D4D · Crystal structure of Thermus thermophilus product complex for transcription initiation… · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9Z9H6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q72L95
- Elsewhere: RCSB PDB 5D4D · PDBe 5D4D · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q72L95
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