Research workbench
Rr (RSIG)2-(C-di-GMP)2-whig complex
Analyse Rr (RSIG)2-(C-di-GMP)2-whig complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LQ4
- Type
- protein
- Length
- 343 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rsig; Whig
- UniProt
- A0A023X3Z4
- Ligands
- C2E
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Rsig | protein | 77 | 66% helix, 1% strand | A0A023X3Z4 |
| T | Rsig | protein | 74 | 77% helix, 0% strand | A0A023X3Z4 |
| A | Whig | protein | 192 | 76% helix, 1% strand | — |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains D, T, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.58 | 0.81 | 30 | C2E |
| 2 | 326 | 0.54 | 0.75 | 39 | empty |
| 3 | 121 | 0.50 | 0.80 | 25 | empty |
| 4 | 80 | 0.42 | 0.79 | 18 | empty |
| 5 | 109 | 0.35 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- D–T · 1807 Ų buried · 11 hydrogen bonds · protein-protein
- D–A · 1614 Ų buried · 11 hydrogen bonds · protein-protein
- T–A · 985 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7LQ4 · Rr (RsiG)2-(c-di-GMP)2-WhiG complex · the same entry in another collection · chain D against D, TM-score 1.00
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 A0A023X3Z4
- Elsewhere: RCSB PDB 7LQ4 · PDBe 7LQ4 · UniProt A0A023X3Z4
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