MolNFT v1 · #76616 · protein
Crystal structure of archaeal SPT4/5 bound to the rnap clamp domain
3QQC · DNA-directed RNA polymerase subunit B, DNA-directed RNA…: “Crystal structure of archaeal SPT4/5 bound to the rnap clamp domain”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.70). MolNFT v1 #76616 on GenesisL1: 3D…
- PDB
- 3QQC
- Type
- protein
- Length
- 521 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit B, DNA-directed RNA polymerase subunit a'…
- UniProt
- Q8U0M3, Q8U0M4, Q8U0M5, Q8TZK1, Q8U440
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit B, DNA-directed RNA polymerase subunit a', DNA-directed RNA polymerase subunit a'' | protein | 381 | 35% helix, 19% strand | Q8U0M3, Q8U0M4, Q8U0M5 |
| D | Transcription antitermination protein nusg | protein | 82 | 33% helix, 18% strand | Q8TZK1 |
| E | DNA-directed RNA polymerase, subunit E'' | protein | 58 | 10% helix, 28% strand | Q8U440 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.70 | 0.86 | 33 | empty |
| 2 | 213 | 0.59 | 0.80 | 32 | empty |
| 3 | 317 | 0.57 | 0.76 | 30 | empty |
| 4 | 60 | 0.45 | 0.83 | 18 | empty |
| 5 | 118 | 0.44 | 0.77 | 18 | empty |
Interfaces
2 interfaces between chains.
- D–E · 976 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3QQC · Crystal structure of archaeal Spt4/5 bound to the RNAP clamp domain · 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 E against A, TM-score 0.94
- Q8TZK1 · AlphaFold monomer V2.0 prediction for transcription elongation factor SPT5 (Q8TZK1) · a predicted model of the same protein · chain D against A, TM-score 0.94
- Q8U0M5 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit a'' (Q8U0M5) · a predicted model of the same protein · chain A against A, TM-score 0.21
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 Q8U0M3
- Every structure of UniProt Q8U0M4
- Every structure of UniProt Q8U0M5
- Every structure of UniProt Q8TZK1
- Every structure of UniProt Q8U440
- Elsewhere: RCSB PDB 3QQC · PDBe 3QQC · UniProt Q8U0M3 · UniProt Q8U0M4 · UniProt Q8U0M5 · UniProt Q8TZK1 · UniProt Q8U440
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