Research workbench
Crystal structure of thioesterase complexed with coenzyme a and zn from thermus thermophilus HB8
Analyse Crystal structure of thioesterase complexed with coenzyme a and zn from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CYE
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative thioesterase
- EC
- 3.1.2.-
- UniProt
- Q5SH84
- Ligands
- COA, ZN
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative thioesterase (EC 3.1.2.-) | protein | 130 | 28% helix, 44% strand | Q5SH84 |
| C | Putative thioesterase (EC 3.1.2.-) | protein | 133 | 27% helix, 43% strand | Q5SH84 |
| D | Putative thioesterase (EC 3.1.2.-) | protein | 125 | 26% helix, 44% strand | Q5SH84 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains B, D, A, C
- ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.85 | 0.98 | 28 | empty |
| 2 | 130 | 0.55 | 0.82 | 25 | empty |
| 3 | 115 | 0.52 | 0.82 | 26 | empty |
| 4 | 124 | 0.51 | 0.81 | 26 | empty |
| 5 | 116 | 0.49 | 0.80 | 23 | ZN |
Interfaces
6 interfaces between chains.
- A–C · 1046 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1045 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1045 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1037 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 392 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 2CYE · Crystal structure of Thioesterase complexed with coenzyme A and Zn from Thermus… · 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 Q5SH84
- Elsewhere: RCSB PDB 2CYE · PDBe 2CYE · UniProt Q5SH84
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