Research workbench
Crystal structure of the pyridoxal-5'-phosphate dependent protein yhfx from escherichia COLI
Analyse Crystal structure of the pyridoxal-5'-phosphate dependent protein yhfx from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KBX
- Type
- protein
- Length
- 386 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein yhfx
- UniProt
- P45550
- Ligands
- ACE, SO4, CL
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein yhfx | protein | 386 | 33% helix, 26% strand | P45550 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.58 | 0.78 | 31 | SO4 |
Modifications
Observed in the structure: 6 modified, 1 covalent (engineered, cofactor, covalent ligand).
Compared structures
- 4KBX · Crystal structure of the pyridoxal-5'-phosphate dependent protein yhfx from escherichia… · the same entry in another collection · chain A against A, TM-score 1.00
- P45550 · AlphaFold monomer V2.0 prediction for uncharacterized protein yhfx (P45550) · a predicted model of the same protein · 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 P45550
- Elsewhere: RCSB PDB 4KBX · PDBe 4KBX · UniProt P45550
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