MolNFT v1 · #124047 · protein
Crystals structure of acyl-CoA oxidase-1 in caenorhabditis elegans, apo form-I
5K3G · Acyl-coenzyme a oxidase: “Crystals structure of acyl-CoA oxidase-1 in caenorhabditis elegans, apo form-I”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #124047 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5K3G
- Type
- protein
- Length
- 2,518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-coenzyme a oxidase
- UniProt
- O62140
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-coenzyme a oxidase | protein | 629 | 59% helix, 10% strand | O62140 |
| B | Acyl-coenzyme a oxidase | protein | 633 | 58% helix, 10% strand | O62140 |
| C | Acyl-coenzyme a oxidase | protein | 630 | 59% helix, 10% strand | O62140 |
| D | Acyl-coenzyme a oxidase | protein | 626 | 58% helix, 10% strand | O62140 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.85 | 0.86 | 107 | empty |
| 2 | 493 | 0.85 | 0.91 | 52 | empty |
| 3 | 892 | 0.85 | 0.86 | 73 | empty |
| 4 | 514 | 0.84 | 0.91 | 56 | empty |
| 5 | 208 | 0.68 | 0.86 | 38 | empty |
Interfaces
3 interfaces between chains.
- C–D · 5664 Ų buried · 74 hydrogen bonds · protein-protein
- A–B · 5588 Ų buried · 73 hydrogen bonds · protein-protein
- A–C · 448 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5K3G · Crystals structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans, Apo form-I · the same entry in another collection · chain D against D, TM-score 1.00
- O62140 · AlphaFold monomer V2.0 prediction for acyl-coenzyme a oxidase acox-1.1 (O62140) · a predicted model of the same protein · chain C 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 O62140
- Elsewhere: RCSB PDB 5K3G · PDBe 5K3G · UniProt O62140
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