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Structure of the periplasmic domain of the motb L119P mutant from salmonella (crystal form 1)
Analyse Structure of the periplasmic domain of the motb L119P mutant from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y3Z
- Type
- protein
- Length
- 283 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Motility protein B
- UniProt
- P55892
- Ligands
- ARG
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Motility protein B | protein | 141 | 33% helix, 23% strand | P55892 |
| B | Motility protein B | protein | 142 | 30% helix, 25% strand | P55892 |
Ligands and binding sites
- ARG · Arginine · ligand · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.72 | 0.86 | 32 | IMD |
| 2 | 109 | 0.66 | 0.90 | 29 | IMD |
| 3 | 64 | 0.44 | 0.82 | 17 | empty |
| 4 | 60 | 0.34 | 0.78 | 20 | empty |
| 5 | 72 | 0.34 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1386 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5Y3Z · Structure of the periplasmic domain of the MotB L119P mutant from Salmonella (crystal… · the same entry in another collection · chain B against B, TM-score 1.00
- P55892 · AlphaFold monomer V2.0 prediction for motility protein B (P55892) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P55892
- Elsewhere: RCSB PDB 5Y3Z · PDBe 5Y3Z · UniProt P55892
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