MolNFT v1 · #18378 · protein
Crystal structure analysis of the selenomethionine labelled 2-enoyl- CoA hydratase 2 domain of candida tropicalis multifunctional enzyme type 2
1PN2 · Peroxisomal hydratase-dehydrogenase-epimerase: “Crystal structure analysis of the selenomethionine labelled 2-enoyl- CoA hydratase 2 domain of candida…”. X-ray diffraction, 16 pockets (best druggability 0.69). MolNFT v1 #18378 on…
- PDB
- 1PN2
- Type
- protein
- Length
- 1,081 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
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal hydratase-dehydrogenase-epimerase (EC 4.2.1.-) | protein | 272 | 24% helix, 36% strand | P22414 |
| B | Peroxisomal hydratase-dehydrogenase-epimerase (EC 4.2.1.-) | protein | 270 | 27% helix, 37% strand | P22414 |
| C | Peroxisomal hydratase-dehydrogenase-epimerase (EC 4.2.1.-) | protein | 267 | 25% helix, 37% strand | P22414 |
| D | Peroxisomal hydratase-dehydrogenase-epimerase (EC 4.2.1.-) | protein | 272 | 25% helix, 36% strand | P22414 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.69 | 0.80 | 50 | empty |
| 2 | 465 | 0.67 | 0.79 | 45 | EDO |
| 3 | 479 | 0.67 | 0.78 | 45 | empty |
| 4 | 189 | 0.64 | 0.84 | 40 | empty |
| 5 | 389 | 0.59 | 0.75 | 47 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1168 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1157 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1PN2 · Crystal structure analysis of the selenomethionine labelled 2-enoyl-CoA hydratase 2… · 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 D 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 1PN2 · PDBe 1PN2 · UniProt P22414
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.