MolNFT v1 · #134308 · protein
Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from escherichia COLI in complex with hexanoyl-CoA
5T06 · Acyl-CoA thioester hydrolase ybgc: “Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from escherichia COLI in complex with…”. X-ray diffraction, 1 ligand (HXC), 8 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 5T06
- Type
- protein
- Length
- 515 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA thioester hydrolase ybgc
- EC
- 3.1.2.-
- UniProt
- P0A8Z5
- Ligands
- HXC
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA thioester hydrolase ybgc (EC 3.1.2.-) | protein | 130 | 25% helix, 44% strand | P0A8Z5 |
| B, D | Acyl-CoA thioester hydrolase ybgc (EC 3.1.2.-) | protein | 129 | 26% helix, 40% strand | P0A8Z5 |
| C | Acyl-CoA thioester hydrolase ybgc (EC 3.1.2.-) | protein | 127 | 26% helix, 42% strand | P0A8Z5 |
Ligands and binding sites
- HXC · Hexanoyl-coenzyme A · ligand · chains A, B, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.87 | 0.95 | 39 | empty |
| 2 | 392 | 0.78 | 0.87 | 51 | EDO |
| 3 | 227 | 0.76 | 0.90 | 33 | HXC |
| 4 | 455 | 0.75 | 0.84 | 48 | EDO |
| 5 | 425 | 0.75 | 0.84 | 49 | EDO |
Interfaces
6 interfaces between chains.
- A–C · 929 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 857 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 836 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 793 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 382 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5T06 · Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from Escherichia coli… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A8Z5 · AlphaFold monomer V2.0 prediction for acyl-CoA thioester hydrolase ybgc (P0A8Z5) · 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 P0A8Z5
- Elsewhere: RCSB PDB 5T06 · PDBe 5T06 · UniProt P0A8Z5
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