MolNFT v1 · #134309 · protein
Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from escherichia COLI in complex with decanoyl-CoA
5T07 · 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 (MFK), 8 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 5T07
- Type
- protein
- Length
- 520 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
- MFK
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA thioester hydrolase ybgc (EC 3.1.2.-) | protein | 131 | 25% helix, 42% strand | P0A8Z5 |
| B | Acyl-CoA thioester hydrolase ybgc (EC 3.1.2.-) | protein | 130 | 26% helix, 44% strand | P0A8Z5 |
| C | Acyl-CoA thioester hydrolase ybgc (EC 3.1.2.-) | protein | 129 | 25% helix, 42% strand | P0A8Z5 |
| D | Acyl-CoA thioester hydrolase ybgc (EC 3.1.2.-) | protein | 130 | 25% helix, 44% strand | P0A8Z5 |
Ligands and binding sites
- MFK · decanoyl-CoA · ligand · 3 copies · chains A, C, D, B
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 | 427 | 0.87 | 0.95 | 38 | empty |
| 2 | 253 | 0.79 | 0.91 | 36 | MFK |
| 3 | 275 | 0.78 | 0.90 | 38 | MFK |
| 4 | 242 | 0.78 | 0.90 | 38 | MFK |
| 5 | 395 | 0.76 | 0.86 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1001 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 943 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 912 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 881 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 350 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 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 5T07 · PDBe 5T07 · UniProt P0A8Z5
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