MolNFT v1 · #181984 · protein
Crystal structure of staphylococcus aureus cystathionine gamma lyase, holoenzyme with bound NL1
7MCT · Bifunctional cystathionine gamma-LYASE/HOMOCYSTEINE…: “Crystal structure of staphylococcus aureus cystathionine gamma lyase, holoenzyme with bound NL1”. X-ray diffraction, 3 ligands (LB6, PLP, NA), 3 pockets (best druggability…
- PDB
- 7MCT
- Type
- protein
- Length
- 380 residues
- Chains
- 1
- 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
- LB6, PLP, NA
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Bifunctional cystathionine gamma-LYASE/HOMOCYSTEINE desulfhydrase (EC 4.4.1.1, 4.4.1.8, 2.5.1.48) | protein | 380 | 40% helix, 17% strand | X5E0F1 |
Ligands and binding sites
- LB6 · N-[(6-bromo-1H-indol-1-yl)acetyl]glycine · ligand · 5 copies · chains H
- PLP · Pyridoxal-5'-phosphate · ligand · chains H
- NA · Sodium ion · metal · 2 copies · chains H
- GOL · Glycerol · additive · 5 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.55 | 0.77 | 28 | LB6 |
| 2 | 114 | 0.40 | 0.75 | 18 | LB6 |
| 3 | 51 | 0.28 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 1 cofactor, 1 modified (pyridoxal phosphate Schiff base, cofactor).
Compared structures
- 7MCT · Crystal structure of Staphylococcus aureus Cystathionine gamma lyase, Holoenzyme with… · the same entry in another collection · chain H against H, 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 7MCT · PDBe 7MCT · UniProt X5E0F1
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