MolNFT v1 · #181991 · protein

Crystal structure of staphylococcus aureus cystathionine gamma lyase holoenzyme Y103N mutant co-crystallized with NL1

7MD6 · Bifunctional cystathionine gamma-LYASE/HOMOCYSTEINE…: “Crystal structure of staphylococcus aureus cystathionine gamma lyase holoenzyme Y103N mutant co-crystallized…”. X-ray diffraction, 2 ligands (LB6, NA), 3 pockets (best…

PDB: 7MD6
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, NA
Pockets: 3 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 39% 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	39% helix, 17% strand	X5E0F1

Ligands and binding sites

LB6 · N-[(6-bromo-1H-indol-1-yl)acetyl]glycine · ligand · 7 copies · chains H
NA · Sodium ion · metal · 2 copies · chains H
FLC · Citrate anion · additive · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	156	0.47	0.77	26	LB6
2	120	0.41	0.75	21	LB6
3	53	0.28	0.75	16	FLC

Modifications

Observed in the structure: 1 modified (cofactor).

Compared structures

7MD6 · Crystal structure of Staphylococcus aureus cystathionine gamma lyase holoenzyme Y103N… · 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 7MD6 · PDBe 7MD6 · UniProt X5E0F1

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