Research workbench
Complex structure of WHIB1 and region 4 of siga in C2221 space group
Analyse Complex structure of WHIB1 and region 4 of siga in C2221 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ONO
- Type
- protein
- Length
- 285 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription regulator WHIB1; RNA polymerase sigma factor siga
- UniProt
- P9WF43, P9WGI1
- Ligands
- SF4
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription regulator WHIB1 | protein | 72 | 58% helix, 3% strand | P9WF43 |
| B | RNA polymerase sigma factor siga | protein | 69 | 71% helix, 0% strand | P9WGI1 |
| C | Transcription regulator WHIB1 | protein | 74 | 59% helix, 3% strand | P9WF43 |
| D | RNA polymerase sigma factor siga | protein | 70 | 70% helix, 0% strand | P9WGI1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.35 | 0.76 | 22 | empty |
| 2 | 56 | 0.26 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 763 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 747 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 678 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 6ONO · Complex structure of WhiB1 and region 4 of SigA in C2221 space group · the same entry in another collection · chain D against D, TM-score 1.00
- P9WF43 · AlphaFold monomer V2.0 prediction for transcriptional regulator WHIB1 (P9WF43) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P9WGI1 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor siga (P9WGI1) · a predicted model of the same protein · chain B against A, TM-score 0.75
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 P9WF43
- Every structure of UniProt P9WGI1
- Elsewhere: RCSB PDB 6ONO · PDBe 6ONO · UniProt P9WF43 · UniProt P9WGI1
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