MolNFT v1 · #185510 · protein
Benzoylsuccinyl-CoA thiolase with coenzyme a
7PYT · Benzoylsuccinyl-CoA thiolase subunit: “Benzoylsuccinyl-CoA thiolase with coenzyme a”. X-ray diffraction, 5 ligands (COA, ZN, MG), 6 pockets (best druggability 0.87). MolNFT v1 #185510 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7PYT
- Type
- protein
- Length
- 1,051 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoylsuccinyl-CoA thiolase subunit
- UniProt
- Q39VG2, Q39VG1
- Ligands
- COA, ZN, MG, PO4, CL
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzoylsuccinyl-CoA thiolase subunit | protein | 134 | 0% helix, 46% strand | Q39VG2 |
| B, D | Benzoylsuccinyl-CoA thiolase subunit | protein | 392 | 37% helix, 19% strand | Q39VG1 |
| C | Benzoylsuccinyl-CoA thiolase subunit | protein | 133 | 0% helix, 45% strand | Q39VG2 |
Ligands and binding sites
- COA · Coenzyme A · ligand · chains C, D
- ZN · Zinc ion · metal · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains B
- PO4 · Phosphate ion · ion · 2 copies · chains B, D
- CL · Chloride ion · ion · chains D
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 4 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.87 | 0.89 | 128 | COA, CL |
| 2 | 309 | 0.78 | 0.89 | 41 | PE8 |
| 3 | 124 | 0.50 | 0.80 | 25 | empty |
| 4 | 148 | 0.50 | 0.79 | 25 | empty |
| 5 | 82 | 0.34 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–D · 2163 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 1565 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1539 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 347 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 307 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7PYT · Benzoylsuccinyl-CoA thiolase with coenzyme A · 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 Q39VG2
- Every structure of UniProt Q39VG1
- Elsewhere: RCSB PDB 7PYT · PDBe 7PYT · UniProt Q39VG2 · UniProt Q39VG1
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