Research workbench
Fe-S cluster-bound transcription activator WHIB7 in complex with the SIGMAAR4-rnap beta flap tip chimera
Analyse Fe-S cluster-bound transcription activator WHIB7 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KUG
- Type
- protein
- Length
- 316 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 0.70
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Probable transcriptional regulator WHIB7 | protein | 64 | 47% helix, 13% strand | Q6MX01 |
| B | RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera (EC 2.7.7.6) | protein | 92 | 73% helix, 0% strand | A0A654TMB9, A1KGE7 |
| D | RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera (EC 2.7.7.6) | protein | 96 | 71% helix, 0% strand | A0A654TMB9, A1KGE7 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.70 | 0.76 | 64 | empty |
| 2 | 72 | 0.36 | 0.77 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 619 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 611 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 233 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 113 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 7KUG · Fe-S cluster-bound transcription activator WhiB7 in complex with the SigmaAr4-RNAP Beta… · 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 0.91
- 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 7KUG · PDBe 7KUG · UniProt Q6MX01 · UniProt A0A654TMB9 · UniProt A1KGE7
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