MolNFT v1 · #18380 · protein
Crystal structure of 2-enoyl-CoA hydratase 2 domain of candida tropicalis multifunctional enzyme type 2 complexed with (3R)- hydroxydecanoyl-CoA.
1PN4 · Peroxisomal hydratase-dehydrogenase-epimerase: “Crystal structure of 2-enoyl-CoA hydratase 2 domain of candida tropicalis multifunctional enzyme type 2…”. X-ray diffraction, 1 ligand (HDC), 14 pockets (best druggability 0.76).…
- PDB
- 1PN4
- Type
- protein
- Length
- 1,064 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal hydratase-dehydrogenase-epimerase
- EC
- 4.2.1.-
- UniProt
- P22414
- Ligands
- HDC
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisomal hydratase-dehydrogenase-epimerase (EC 4.2.1.-) | protein | 272 | 28% helix, 36% strand | P22414 |
| C | Peroxisomal hydratase-dehydrogenase-epimerase (EC 4.2.1.-) | protein | 247 | 24% helix, 36% strand | P22414 |
| D | Peroxisomal hydratase-dehydrogenase-epimerase (EC 4.2.1.-) | protein | 273 | 27% helix, 36% strand | P22414 |
Ligands and binding sites
- HDC · 3R-hydroxydecanoyl-coenzyme A · ligand · 3 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.76 | 0.83 | 62 | HDC, EDO |
| 2 | 735 | 0.70 | 0.77 | 73 | empty |
| 3 | 370 | 0.67 | 0.80 | 55 | HDC |
| 4 | 319 | 0.66 | 0.81 | 51 | HDC, EDO |
| 5 | 288 | 0.63 | 0.80 | 48 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1174 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1166 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 415 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1PN4 · Crystal structure of 2-enoyl-CoA hydratase 2 domain of Candida tropicalis multifunctional… · the same entry in another collection · chain D against D, TM-score 1.00
- P22414 · AlphaFold monomer V2.0 prediction for peroxisomal hydratase- dehydrogenase-epimerase… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P22414
- Elsewhere: RCSB PDB 1PN4 · PDBe 1PN4 · UniProt P22414
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