Research workbench
X-ray crystal structure of E. COLI ybdb complexed with phenacyl-CoA
Analyse X-ray crystal structure of E. COLI ybdb complexed with phenacyl-CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K4C
- Type
- protein
- Length
- 548 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proofreading thioesterase enth
- EC
- 3.1.2.-
- UniProt
- P0A8Y8
- Ligands
- 0FQ
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Proofreading thioesterase enth (EC 3.1.2.-) | protein | 137 | 20% helix, 41% strand | P0A8Y8 |
Ligands and binding sites
- 0FQ · phenacyl coenzyme A · ligand · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.80 | 0.86 | 88 | 0FQ |
| 2 | 502 | 0.80 | 0.87 | 83 | 0FQ |
Interfaces
6 interfaces between chains.
- A–D · 1413 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1400 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 570 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 548 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 266 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4K4C · X-ray crystal structure of E. coli YbdB complexed with phenacyl-CoA · the same entry in another collection · chain D against D, TM-score 1.00
- P0A8Y8 · AlphaFold monomer V2.0 prediction for proofreading thioesterase enth (P0A8Y8) · 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 P0A8Y8
- Elsewhere: RCSB PDB 4K4C · PDBe 4K4C · UniProt P0A8Y8
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