Research workbench
Crystal structure of 4-COUMARATE:COA ligase delta-V341 mutant complexed with feruloyl adenylate
Analyse Crystal structure of 4-COUMARATE:COA ligase delta-V341 mutant complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BSW
- Type
- protein
- Length
- 1,052 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-coumarate--CoA ligase 2
- EC
- 6.2.1.12
- UniProt
- O24146
- Ligands
- 4UW
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-coumarate--CoA ligase 2 (EC 6.2.1.12) | protein | 526 | 31% helix, 25% strand | O24146 |
| B | 4-coumarate--CoA ligase 2 (EC 6.2.1.12) | protein | 526 | 32% helix, 26% strand | O24146 |
Ligands and binding sites
- 4UW · 5'-O-[(R)-hydroxy{[(2E)-3-(5-methoxy-4-oxocyclohexa-1,5-dien-1-yl)prop-2-enoyl]oxy}phosphoryl]adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.83 | 0.84 | 125 | 4UW |
| 2 | 671 | 0.81 | 0.85 | 83 | 4UW |
| 3 | 222 | 0.59 | 0.80 | 29 | empty |
| 4 | 254 | 0.54 | 0.76 | 35 | empty |
| 5 | 232 | 0.52 | 0.76 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 495 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5BSW · Crystal structure of 4-coumarate:CoA ligase delta-V341 mutant complexed with feruloyl… · the same entry in another collection · chain A against A, TM-score 1.00
- O24146 · AlphaFold monomer V2.0 prediction for 4-coumarate--CoA ligase 2 (O24146) · a predicted model of the same protein · chain B 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 O24146
- Elsewhere: RCSB PDB 5BSW · PDBe 5BSW · UniProt O24146
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