Research workbench
Crystal structure of protein of unknown function yfih from shigella flexneri 2A str. 2457T
Analyse Crystal structure of protein of unknown function yfih from shigella flexneri 2A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XAF
- Type
- protein
- Length
- 483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orf, conserved hypothetical protein
- UniProt
- Q83K13
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orf, conserved hypothetical protein | protein | 242 | 25% helix, 26% strand | Q83K13 |
| B | Orf, conserved hypothetical protein | protein | 241 | 25% helix, 27% strand | Q83K13 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.80 | 0.81 | 96 | ZN, ACT, GOL |
| 2 | 192 | 0.49 | 0.76 | 28 | ACT, GOL |
Interfaces
1 interface between chains.
- A–B · 575 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1XAF · Crystal Structure of Protein of Unknown Function YfiH from Shigella flexneri 2a str. 2457T · 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 Q83K13
- Elsewhere: RCSB PDB 1XAF · PDBe 1XAF · UniProt Q83K13
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