MolNFT v1 · #9932 · protein
Crystal structure of cystathionine beta-lyase from arabidopsis thaliana
1IBJ: “Crystal structure of cystathionine beta-lyase from arabidopsis thaliana”. X-ray diffraction, 3 ligands (PLP, CO3, SO4), 5 pockets (best druggability 0.73). MolNFT v1 #9932 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1IBJ
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-lyase
- EC
- 4.4.1.8
- UniProt
- P53780
- Ligands
- PLP, CO3, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cystathionine beta-lyase (EC 4.4.1.8) | protein | 380 | 34% helix, 15% strand | P53780 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, C
- CO3 · Carbonate ion · ion · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.73 | 0.81 | 74 | CO3, PLP |
| 2 | 503 | 0.70 | 0.80 | 65 | CO3, PLP |
| 3 | 64 | 0.70 | 0.97 | 20 | empty |
| 4 | 84 | 0.52 | 0.84 | 23 | empty |
| 5 | 64 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 2619 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1IBJ · Crystal structure of cystathionine beta-lyase from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- P53780 · AlphaFold monomer V2.0 prediction for cystathionine beta-lyase, chloroplastic (P53780) · a predicted model of the same protein · chain A 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 P53780
- Elsewhere: RCSB PDB 1IBJ · PDBe 1IBJ · UniProt P53780
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