MolNFT v1 · #160270 · protein
Structure of S. venezuelae rsig-whig-(ci-di-gmp) complex, P64 crystal form
6PFJ · Amfc protein: “Structure of S. venezuelae rsig-whig-(ci-di-gmp) complex, P64 crystal form”. X-ray diffraction, 1 ligand (C2E), 5 pockets (best druggability 0.69). MolNFT v1 #160270 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6PFJ
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amfc protein; RNA polymerase sigma factor
- UniProt
- F2RFR7, A0A3N1Q704
- Ligands
- C2E
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Amfc protein | protein | 149 | 74% helix, 0% strand | F2RFR7 |
| A | RNA polymerase sigma factor | protein | 219 | 73% helix, 0% strand | A0A3N1Q704 |
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 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.69 | 0.79 | 51 | C2E |
| 2 | 114 | 0.61 | 0.86 | 15 | empty |
| 3 | 178 | 0.54 | 0.79 | 28 | empty |
| 4 | 59 | 0.36 | 0.78 | 13 | empty |
| 5 | 56 | 0.30 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- T–A · 2456 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6PFJ · Structure of S. venezuelae RsiG-WhiG-(ci-di-GMP) complex, P64 crystal form · the same entry in another collection · chain T against T, 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 F2RFR7
- Every structure of UniProt A0A3N1Q704
- Elsewhere: RCSB PDB 6PFJ · PDBe 6PFJ · UniProt F2RFR7 · UniProt A0A3N1Q704
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.