MolNFT v1 · #146854 · protein + RNA
Structure of a rho-nusg kow domain complex
6DUQ · Transcription termination factor rho: “Structure of a rho-nusg kow domain complex”. X-ray diffraction, 3 ligands (ADP, BEF, MG), 20 pockets (best druggability 0.77). MolNFT v1 #146854 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DUQ
- Type
- protein + RNA
- Length
- 5,466 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription termination factor rho; Transcription TERMINATION/ANTITERMINATION protein…
- EC
- 3.6.4.-
- UniProt
- F4TMM7, F4T6L5
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B, H, D, F, J | Transcription termination factor rho (EC 3.6.4.-) | protein | 409 | 43% helix, 22% strand | F4TMM7 |
| A, G, C, I, K, E | Transcription termination factor rho (EC 3.6.4.-) | protein | 414 | 42% helix, 22% strand | F4TMM7 |
| M, N, O, P, Q, R, S, T, U, V, W, X | Transcription TERMINATION/ANTITERMINATION protein nusg | protein | 43 | 7% helix, 58% strand | F4T6L5 |
| Y, Z | RU12 | rna | 6 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains L, K, A, F, G, B, H, C, I, D, J, E
- BEF · Beryllium trifluoride ion · ligand · 12 copies · chains L, K, A, F, G, B, H, C, I, D, J, E
- MG · Magnesium ion · metal · 12 copies · chains L, A, G, B, H, C, I, D, K, F, J, E
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 | 873 | 0.77 | 0.80 | 90 | ADP, MG, BEF |
| 2 | 206 | 0.77 | 0.91 | 31 | empty |
| 3 | 177 | 0.76 | 0.92 | 30 | empty |
| 4 | 758 | 0.76 | 0.81 | 75 | ADP, MG, BEF |
| 5 | 724 | 0.76 | 0.81 | 73 | ADP, MG, BEF |
Interfaces
40 interfaces between chains.
- B–C · 1561 Ų buried · 27 hydrogen bonds · protein-protein
- L–G · 1550 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 1546 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1537 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 1528 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6DUQ · Structure of a Rho-NusG KOW domain complex · the same entry in another collection · chain A against A, 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 F4TMM7
- Every structure of UniProt F4T6L5
- Elsewhere: RCSB PDB 6DUQ · PDBe 6DUQ · UniProt F4TMM7 · UniProt F4T6L5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.