MolNFT v1 · #181995 · protein
Crystal structure of staphylococcus aureus cystathionine gamma lyase holoenzyme Y103A mutant co-crystallized with NL2
7MDB · Bifunctional cystathionine gamma-LYASE/HOMOCYSTEINE…: “Crystal structure of staphylococcus aureus cystathionine gamma lyase holoenzyme Y103A mutant co-crystallized…”. X-ray diffraction, 3 ligands (YXA, PLP, NA), 2 pockets (best…
- PDB
- 7MDB
- 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
- YXA, PLP, NA
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 41% 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 | 41% helix, 17% strand | X5E0F1 |
Ligands and binding sites
- YXA · 5-[(6-bromo-1H-indol-1-yl)methyl]-2-methylfuran-3-carboxylic acid · ligand · 2 copies · chains H
- PLP · Pyridoxal-5'-phosphate · ligand · chains H
- NA · Sodium ion · metal · 2 copies · chains H
- CAC · Cacodylate ion · additive · 2 copies · chains H
- GOL · Glycerol · additive · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.50 | 0.76 | 32 | YXA, CAC |
| 2 | 120 | 0.41 | 0.75 | 21 | empty |
Modifications
Observed in the structure: 1 cofactor, 1 modified (pyridoxal phosphate Schiff base, cofactor).
Compared structures
- 7MDB · Crystal structure of Staphylococcus aureus cystathionine gamma lyase holoenzyme Y103A… · 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 7MDB · PDBe 7MDB · UniProt X5E0F1
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