MolNFT v1 · #63301 · protein
Crystal structure of HTHEM2(UNDECAN-2-one-CoA) complex
3F5O · Thioesterase superfamily member 2: “Crystal structure of HTHEM2(UNDECAN-2-one-CoA) complex”. X-ray diffraction, 3 ligands (UOC, COA, CL), 9 pockets (best druggability 0.86). MolNFT v1 #63301 on GenesisL1: 3D structure, binding sites…
- PDB
- 3F5O
- Type
- protein
- Length
- 1,098 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioesterase superfamily member 2
- UniProt
- Q9NPJ3
- Ligands
- UOC, COA, CL
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F, H | Thioesterase superfamily member 2 | protein | 138 | 28% helix, 41% strand | Q9NPJ3 |
| B, G | Thioesterase superfamily member 2 | protein | 136 | 26% helix, 43% strand | Q9NPJ3 |
| C, D | Thioesterase superfamily member 2 | protein | 137 | 28% helix, 42% strand | Q9NPJ3 |
Ligands and binding sites
- UOC · undecan-2-one · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- COA · Coenzyme A · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D, E, F, G, H
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.86 | 0.87 | 111 | CL, UOC |
| 2 | 347 | 0.67 | 0.81 | 41 | CL, UOC, COA, P6G |
| 3 | 343 | 0.67 | 0.81 | 38 | CL, UOC, COA, P6G |
| 4 | 330 | 0.67 | 0.81 | 39 | CL, UOC, COA, P6G |
| 5 | 307 | 0.65 | 0.81 | 41 | UOC, COA |
Interfaces
15 interfaces between chains.
- E–F · 1257 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1239 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1232 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1222 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 619 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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 Q9NPJ3
- Elsewhere: RCSB PDB 3F5O · PDBe 3F5O · UniProt Q9NPJ3
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