Research workbench
Crystal structure analysis of human clybl in complex with propionyl- CoA
Analyse Crystal structure analysis of human clybl in complex with propionyl- CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VXO
- Type
- protein
- Length
- 894 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate lyase subunit beta-like protein, mitochondrial
- UniProt
- Q8N0X4
- Ligands
- 1VU, PO4
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Citrate lyase subunit beta-like protein, mitochondrial | protein | 298 | 51% helix, 16% strand | Q8N0X4 |
Ligands and binding sites
- 1VU · propionyl Coenzyme A · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains A, B, C
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.72 | 0.87 | 40 | 1VU |
| 2 | 278 | 0.72 | 0.86 | 49 | 1VU |
| 3 | 229 | 0.70 | 0.86 | 45 | 1VU |
| 4 | 616 | 0.68 | 0.77 | 72 | EDO, PG4 |
| 5 | 493 | 0.65 | 0.77 | 61 | EDO, PG4 |
Interfaces
3 interfaces between chains.
- B–C · 1398 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1396 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1395 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5VXO · Crystal Structure Analysis of human CLYBL in complex with propionyl-CoA · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N0X4 · AlphaFold monomer V2.0 prediction for citramalyl-CoA lyase, mitochondrial (Q8N0X4) · a predicted model of the same protein · chain A 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 Q8N0X4
- Elsewhere: RCSB PDB 5VXO · PDBe 5VXO · UniProt Q8N0X4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.