MolNFT v1 · #181980 · protein
Crystal structure of staphylococcus aureus cystathionine gamma-lyase, holoenzyme dimer
7MCP · Bifunctional cystathionine gamma-LYASE/HOMOCYSTEINE…: “Crystal structure of staphylococcus aureus cystathionine gamma-lyase, holoenzyme dimer”. X-ray diffraction, 2 ligands (PLP, NA), 7 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 7MCP
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional cystathionine gamma-LYASE/HOMOCYSTEINE desulfhydrase
- EC
- 4.4.1.1, 4.4.1.8, 2.5.1.48
- UniProt
- X5E0F1
- Ligands
- PLP, NA
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Bifunctional cystathionine gamma-LYASE/HOMOCYSTEINE desulfhydrase (EC 4.4.1.1, 4.4.1.8, 2.5.1.48) | protein | 380 | 41% helix, 16% strand | X5E0F1 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, H
- NA · Sodium ion · metal · 6 copies · chains A, H
- GOL · Glycerol · additive · 4 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.73 | 0.98 | 25 | empty |
| 2 | 51 | 0.71 | 0.99 | 29 | empty |
| 3 | 297 | 0.60 | 0.79 | 34 | empty |
| 4 | 182 | 0.46 | 0.75 | 29 | empty |
| 5 | 100 | 0.46 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–H · 2603 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 modified (pyridoxal phosphate Schiff base, cofactor).
Compared structures
- 7MCP · Crystal structure of Staphylococcus aureus Cystathionine gamma-lyase, Holoenzyme dimer · the same entry in another collection · chain A against A, 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 X5E0F1
- Elsewhere: RCSB PDB 7MCP · PDBe 7MCP · UniProt X5E0F1
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