MolNFT v1 · #74834 · protein
X-ray crystal structure of pyrococcus furiosus transcription elongation factor SPT4/5
3P8B · DNA-directed RNA polymerase, subunit E'': “X-ray crystal structure of pyrococcus furiosus transcription elongation factor SPT4/5”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.69). MolNFT v1 #74834 on GenesisL1…
- PDB
- 3P8B
- Type
- protein
- Length
- 414 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase, subunit E''; Transcription antitermination protein nusg
- UniProt
- Q8U440, Q8TZK1
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA-directed RNA polymerase, subunit E'' | protein | 60 | 10% helix, 37% strand | Q8U440 |
| B, D | Transcription antitermination protein nusg | protein | 147 | 22% helix, 34% strand | Q8TZK1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- BME · Beta-mercaptoethanol · additive · 6 copies · chains A, B, D
- GOL · Glycerol · additive · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.69 | 0.79 | 68 | GOL, BME |
| 2 | 81 | 0.50 | 0.83 | 17 | BME |
| 3 | 77 | 0.50 | 0.84 | 18 | BME |
| 4 | 89 | 0.38 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1465 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1286 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1279 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3P8B · X-ray crystal structure of Pyrococcus furiosus transcription elongation factor Spt4/5 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8U440 · AlphaFold monomer V2.0 prediction for transcription elongation factor SPT4 (Q8U440) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q8TZK1 · AlphaFold monomer V2.0 prediction for transcription elongation factor SPT5 (Q8TZK1) · a predicted model of the same protein · chain B against A, TM-score 0.60
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 Q8U440
- Every structure of UniProt Q8TZK1
- Elsewhere: RCSB PDB 3P8B · PDBe 3P8B · UniProt Q8U440 · UniProt Q8TZK1
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