Research workbench
Structure of bacillus subtilis inhibitor of motility (MOTI/DGRA)
Analyse Structure of bacillus subtilis inhibitor of motility (MOTI/DGRA) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VX6
- Type
- protein
- Length
- 418 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein ypfa
- UniProt
- P38491
- Ligands
- C2E
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein ypfa | protein | 209 | 8% helix, 49% strand | P38491 |
| B | Uncharacterized protein ypfa | protein | 209 | 9% helix, 55% strand | P38491 |
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 · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.62 | 0.80 | 27 | empty |
| 2 | 98 | 0.39 | 0.76 | 18 | C2E |
| 3 | 80 | 0.35 | 0.76 | 17 | C2E |
Interfaces
1 interface between chains.
- A–B · 812 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5VX6 · Structure of Bacillus subtilis Inhibitor of motility (MotI/DgrA) · the same entry in another collection · chain A against A, TM-score 1.00
- P38491 · AlphaFold monomer V2.0 prediction for uncharacterized protein ypfa (P38491) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P38491
- Elsewhere: RCSB PDB 5VX6 · PDBe 5VX6 · UniProt P38491
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