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Crystal structure of acyl-CoA thioesterase tesB from Yersinia pestis in complex with coenzyme A
Analyse Crystal structure of acyl-CoA thioesterase tesB from Yersinia pestis in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R4U
- Type
- protein
- Length
- 1,078 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Yersinia pestis
- Molecule
- Acyl-CoA thioesterase II
- UniProt
- Q8D151
- Ligands
- COA, NA
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.2 · 4 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA thioesterase II | protein | 277 | 18% helix, 40% strand | Q8D151 |
| D | Acyl-CoA thioesterase II | protein | 264 | 19% helix, 43% strand | Q8D151 |
| C | Acyl-CoA thioesterase II | protein | 272 | 18% helix, 42% strand | Q8D151 |
| B | Acyl-CoA thioesterase II | protein | 265 | 18% helix, 42% strand | Q8D151 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B, D, C
- NA · Sodium ion · metal · 2 copies · chains A, D
- MLA · Malonic acid · additive · chains D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.81 | 0.83 | 87 | COA |
| 2 | 837 | 0.75 | 0.79 | 81 | empty |
| 3 | 560 | 0.72 | 0.80 | 63 | COA |
| 4 | 576 | 0.71 | 0.79 | 61 | empty |
| 5 | 718 | 0.64 | 0.74 | 67 | NA |
Interfaces
4 interfaces between chains.
- A–B · 2621 Ų buried · 59 hydrogen bonds · protein-protein
- D–C · 2596 Ų buried · 58 hydrogen bonds · protein-protein
- C–B · 482 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 479 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4R4U · Crystal structure of acyl-CoA thioesterase tesb from yersinia pestis in complex with… · 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 Q8D151
- Elsewhere: RCSB PDB 4R4U · PDBe 4R4U · UniProt Q8D151
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