MolNFT v1 · #29081 · protein
Crystal structure of peroxisomal trans 2-enoyl CoA reductase
1YXM: “Crystal structure of peroxisomal trans 2-enoyl CoA reductase”. X-ray diffraction, 3 ligands (ADE, SO4, PO4), 15 pockets (best druggability 0.83). MolNFT v1 #29081 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YXM
- Type
- protein
- Length
- 1,135 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal trans 2-enoyl CoA reductase
- EC
- 1.3.1.8
- UniProt
- Q9BY49
- Ligands
- ADE, SO4, PO4
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal trans 2-enoyl CoA reductase (EC 1.3.1.8) | protein | 297 | 48% helix, 14% strand | Q9BY49 |
| B | Peroxisomal trans 2-enoyl CoA reductase (EC 1.3.1.8) | protein | 283 | 47% helix, 15% strand | Q9BY49 |
| C | Peroxisomal trans 2-enoyl CoA reductase (EC 1.3.1.8) | protein | 264 | 44% helix, 16% strand | Q9BY49 |
| D | Peroxisomal trans 2-enoyl CoA reductase (EC 1.3.1.8) | protein | 291 | 49% helix, 14% strand | Q9BY49 |
Ligands and binding sites
- ADE · Adenine · ligand · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.83 | 0.84 | 81 | empty |
| 2 | 703 | 0.78 | 0.83 | 72 | SO4 |
| 3 | 687 | 0.72 | 0.78 | 61 | empty |
| 4 | 555 | 0.70 | 0.79 | 62 | PO4, ADE |
| 5 | 205 | 0.53 | 0.78 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2170 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2146 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1592 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1302 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 764 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1YXM · Crystal structure of peroxisomal trans 2-enoyl CoA reductase · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BY49 · AlphaFold monomer V2.0 prediction for peroxisomal trans-2-enoyl-CoA reductase (Q9BY49) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9BY49
- Elsewhere: RCSB PDB 1YXM · PDBe 1YXM · UniProt Q9BY49
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