MolNFT v1 · #172781 · protein + DNA + RNA
Transcription termination intermediate complex 3 delta nusg
7ADC · Transcription termination factor rho: “Transcription termination intermediate complex 3 delta nusg”. Electron microscopy, 4 ligands (ADP, BEF, MG), 20 pockets (best druggability 0.85). MolNFT v1 #172781 on GenesisL1: 3D structure…
- PDB
- 7ADC
- Type
- protein + DNA + RNA
- Length
- 6,417 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription termination factor rho; Transcription TERMINATION/ANTITERMINATION protein…
- EC
- 3.6.4.-, 2.7.7.6
- UniProt
- A0A0A0GPI6, C3SSN7, P0A7Z4, P0A800, P0A8V4, C3SIA2
- Ligands
- ADP, BEF, MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| f, a, b, c, d, e | Transcription termination factor rho (EC 3.6.4.-) | protein | 417 | 39% helix, 20% strand | A0A0A0GPI6 |
| A | Transcription TERMINATION/ANTITERMINATION protein nusa | protein | 495 | 34% helix, 13% strand | C3SSN7 |
| U | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 235 | 20% helix, 34% strand | P0A7Z4 |
| V | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 321 | 29% helix, 22% strand | P0A7Z4 |
| W | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 63% helix, 0% strand | P0A800 |
| X | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 30% helix, 22% strand | P0A8V4 |
| Y | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1358 | 35% helix, 16% strand | C3SIA2 |
| K | Ntdna | dna | 25 | — | — |
| L | Tdna | dna | 34 | — | — |
| R | Rut RNA | rna | 28 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains f, a, b, c, d, e
- BEF · Beryllium trifluoride ion · ligand · 5 copies · chains f, a, b, c, d, e
- MG · Magnesium ion · metal · 6 copies · chains a, b, c, d, e, Y, R
- ZN · Zinc ion · metal · 2 copies · chains Y
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 | 971 | 0.85 | 0.86 | 105 | empty |
| 2 | 888 | 0.84 | 0.87 | 101 | empty |
| 3 | 478 | 0.83 | 0.91 | 70 | empty |
| 4 | 698 | 0.80 | 0.84 | 78 | empty |
| 5 | 367 | 0.80 | 0.90 | 56 | empty |
Interfaces
37 interfaces between chains.
- X–Y · 8464 Ų buried · 100 hydrogen bonds · protein-protein
- U–V · 2520 Ų buried · 15 hydrogen bonds · protein-protein
- U–X · 1905 Ų buried · 20 hydrogen bonds · protein-protein
- a–b · 1717 Ų buried · 22 hydrogen bonds · protein-protein
- b–c · 1711 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7ADC · Transcription termination intermediate complex 3 delta NusG · the same entry in another collection · chain f against f, 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 A0A0A0GPI6
- Every structure of UniProt C3SSN7
- Every structure of UniProt P0A7Z4
- Every structure of UniProt P0A800
- Every structure of UniProt P0A8V4
- Every structure of UniProt C3SIA2
- Elsewhere: RCSB PDB 7ADC · PDBe 7ADC · UniProt A0A0A0GPI6 · UniProt C3SSN7 · UniProt P0A7Z4 · UniProt P0A800 · UniProt P0A8V4 · UniProt C3SIA2
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