Research workbench
1.9 ångström crystal structure of protein with unknown function from vibrio cholerae.
Analyse 1.9 ångström crystal structure of protein with unknown function from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IQJ
- Type
- protein
- Length
- 387 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- M1QWM5
- Ligands
- TTN, CL, SO4
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein | protein | 131 | 64% helix, 11% strand | M1QWM5 |
| C | Uncharacterized protein | protein | 125 | 68% helix, 12% strand | M1QWM5 |
Ligands and binding sites
- TTN · Tartronate · ligand · 2 copies · chains A, C
- CL · Chloride ion · ion · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains B
- PGE · Triethylene glycol · additive · chains A, B
- ACT · Acetate ion · additive · chains B
- GOL · Glycerol · additive · chains B
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 | 316 | 0.56 | 0.76 | 30 | SO4 |
| 2 | 261 | 0.54 | 0.76 | 28 | TTN |
| 3 | 240 | 0.50 | 0.75 | 31 | SO4 |
| 4 | 68 | 0.30 | 0.74 | 17 | empty |
| 5 | 69 | 0.28 | 0.73 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–C · 451 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 440 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5IQJ · 1.9 Angstrom Crystal Structure of Protein with Unknown Function from Vibrio cholerae. · the same entry in another collection · chain A against A, 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 M1QWM5
- Elsewhere: RCSB PDB 5IQJ · PDBe 5IQJ · UniProt M1QWM5
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