Research workbench
Transcription termination intermediate complex 4
Analyse Transcription termination intermediate complex 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z9S
- Type
- protein + DNA + RNA
- Length
- 6,419 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 | 41% helix, 21% strand | A0A0A0GPI6 |
| A | Transcription TERMINATION/ANTITERMINATION protein nusa | protein | 495 | 35% helix, 13% strand | C3SSN7 |
| U | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 235 | 19% helix, 34% strand | P0A7Z4 |
| V | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 321 | 28% helix, 21% strand | P0A7Z4 |
| W | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 61% 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 | 34% helix, 15% strand | C3SIA2 |
| K | Non template strand | dna | 26 | — | — |
| L | Template strand | dna | 35 | — | — |
| 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 | 879 | 0.85 | 0.87 | 90 | empty |
| 2 | 1058 | 0.84 | 0.85 | 96 | empty |
| 3 | 991 | 0.84 | 0.84 | 77 | empty |
| 4 | 783 | 0.82 | 0.85 | 86 | empty |
| 5 | 619 | 0.81 | 0.87 | 64 | empty |
Interfaces
36 interfaces between chains.
- X–Y · 8232 Ų buried · 89 hydrogen bonds · protein-protein
- U–V · 2538 Ų buried · 29 hydrogen bonds · protein-protein
- U–X · 1964 Ų buried · 20 hydrogen bonds · protein-protein
- b–c · 1799 Ų buried · 16 hydrogen bonds · protein-protein
- a–b · 1745 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
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 6Z9S · PDBe 6Z9S · UniProt A0A0A0GPI6 · UniProt C3SSN7 · UniProt P0A7Z4 · UniProt P0A800 · UniProt P0A8V4 · UniProt C3SIA2
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