Research workbench
X-ray crystal structure of E. COLI ydii complexed with 2,4- dihydroxyphenacyl CoA
Analyse X-ray crystal structure of E. COLI ydii complexed with 2,4- dihydroxyphenacyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K49
- Type
- protein
- Length
- 544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase ydii
- EC
- 3.1.-.-
- UniProt
- P77781
- Ligands
- HFQ
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, D, A | Esterase ydii (EC 3.1.-.-) | protein | 136 | 21% helix, 40% strand | P77781 |
Ligands and binding sites
- HFQ · 2,4-dihydroxyphenacyl coenzyme A · ligand · 4 copies · chains C, B, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.72 | 0.86 | 40 | HFQ |
| 2 | 312 | 0.72 | 0.84 | 43 | HFQ |
| 3 | 257 | 0.71 | 0.86 | 48 | HFQ |
| 4 | 251 | 0.71 | 0.86 | 48 | HFQ |
Interfaces
6 interfaces between chains.
- D–A · 1358 Ų buried · 22 hydrogen bonds · protein-protein
- C–B · 1356 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 576 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 552 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 325 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4K49 · X-ray crystal structure of E. coli YdiI complexed with 2,4-dihydroxyphenacyl CoA · the same entry in another collection · chain C against C, TM-score 1.00
- P77781 · AlphaFold monomer V2.0 prediction for 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (P77781) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P77781
- Elsewhere: RCSB PDB 4K49 · PDBe 4K49 · UniProt P77781
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