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Cystathionine gamma-synthase from nicotiana tabacum

Analyse Cystathionine gamma-synthase from nicotiana tabacum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QGN
Type: protein
Length: 3,184 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (cystathionine gamma-synthase)
EC: 4.2.99.9
UniProt: Q9ZPL5
Ligands: PLP
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Protein (cystathionine gamma-synthase) (EC 4.2.99.9)	protein	398	42% helix, 16% strand	Q9ZPL5

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, C, B, D, E, G, F, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	766	0.83	0.86	117	PLP
2	200	0.83	0.96	20	empty
3	199	0.83	0.96	21	empty
4	971	0.82	0.83	125	empty
5	642	0.81	0.85	98	empty

Interfaces

15 interfaces between chains.

B–D · 2631 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 2630 Å² buried · 16 hydrogen bonds · protein-protein
E–G · 2630 Å² buried · 16 hydrogen bonds · protein-protein
F–H · 2617 Å² buried · 16 hydrogen bonds · protein-protein
E–H · 1919 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (pyridoxal phosphate Schiff base).

Compared structures

1QGN · Cystathionine gamma-synthase from nicotiana tabacum · 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 Q9ZPL5
Elsewhere: RCSB PDB 1QGN · PDBe 1QGN · UniProt Q9ZPL5

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