MolNFT v1 · #116130 · protein + DNA
Crystal structure of thermus thermophilus product complex for transcription initiation with NAD and CTP
5D4D · DNA-directed RNA polymerase subunit alpha: “Crystal structure of thermus thermophilus product complex for transcription initiation with NAD and CTP”. X-ray diffraction, 6 ligands (C, CTP, NAD), 20 pockets (best druggability 0.87).…
- 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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