MolNFT v1 · #180275 · protein + DNA
Transcription activation subcomplex with WHIB7 bound to SIGMAAR4-rnap beta flap tip chimera and DNA
7KUF · Probable transcriptional regulator WHIB7: “Transcription activation subcomplex with WHIB7 bound to SIGMAAR4-rnap beta flap tip chimera and DNA”. X-ray diffraction, 1 ligand (SF4), 2 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 7KUF
- Type
- protein + DNA
- Length
- 194 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable transcriptional regulator WHIB7; RNA polymerase sigma factor, DNA-directed RNA…
- EC
- 2.7.7.6
- UniProt
- Q6MX01, A0A654TMB9, A1KGE7
- Ligands
- SF4
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable transcriptional regulator WHIB7 | protein | 73 | 38% helix, 14% strand | Q6MX01 |
| B | RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera (EC 2.7.7.6) | protein | 85 | 69% helix, 0% strand | A0A654TMB9, A1KGE7 |
| C | DNA (5'- D(*CP*AP*GP*AP*AP*AP*AP*TP*CP*GP*GP*TP*TP*GP*TP*GP*GP*T)-3') | dna | 18 | — | — |
| D | DNA (5'- D(*GP*AP*CP*CP*AP*CP*AP*AP*CP*CP*GP*AP*TP*TP*TP*TP*CP*T)-3') | dna | 18 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.67 | 0.76 | 45 | empty |
| 2 | 113 | 0.50 | 0.81 | 25 | SF4 |
Interfaces
6 interfaces between chains.
- C–D · 757 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–B · 652 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 362 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 333 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 316 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 7KUF · Transcription activation subcomplex with WhiB7 bound to SigmaAr4-RNAP Beta flap tip… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6MX01 · AlphaFold monomer V2.0 prediction for probable transcriptional regulator WHIB7 (Q6MX01) · a predicted model of the same protein · chain A against A, TM-score 0.90
- A1KGE7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (A1KGE7) · a predicted model of the same protein · chain B against A, TM-score 0.47
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 Q6MX01
- Every structure of UniProt A0A654TMB9
- Every structure of UniProt A1KGE7
- Elsewhere: RCSB PDB 7KUF · PDBe 7KUF · UniProt Q6MX01 · UniProt A0A654TMB9 · UniProt A1KGE7
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