Research workbench
Crystal structure of cystathionine gamma-lyase from bacillus cereus atcc 14579
Analyse Crystal structure of cystathionine gamma-lyase from bacillus cereus atcc 14579 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D7O
- Type
- protein
- Length
- 749 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional cystathionine gamma-LYASE/HOMOCYSTEINE desulfhydrase
- UniProt
- A0A5B7VKY7
- Ligands
- PLP, SO4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional cystathionine gamma-LYASE/HOMOCYSTEINE desulfhydrase | protein | 372 | 39% helix, 17% strand | A0A5B7VKY7 |
| B | Bifunctional cystathionine gamma-LYASE/HOMOCYSTEINE desulfhydrase | protein | 377 | 37% helix, 18% strand | A0A5B7VKY7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.75 | 0.99 | 20 | empty |
| 2 | 238 | 0.72 | 0.87 | 36 | SO4 |
| 3 | 277 | 0.63 | 0.81 | 34 | SO4 |
| 4 | 145 | 0.55 | 0.81 | 29 | empty |
| 5 | 152 | 0.51 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2516 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7D7O · Crystal structure of cystathionine gamma-lyase from Bacillus cereus ATCC 14579 · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A5B7VKY7
- Elsewhere: RCSB PDB 7D7O · PDBe 7D7O · UniProt A0A5B7VKY7
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