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Crystal structure of cystathionine gamma synthase from xanthomonas oryzae pv. oryzae in complex with aminoacrylate and cysteine

Analyse Crystal structure of cystathionine gamma synthase from xanthomonas oryzae pv.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LD8
Type: protein
Length: 1,549 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cystathionine gamma-synthase
UniProt: Q5H1U9
Ligands: 0JO, CYS
Pockets: 14 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cystathionine gamma-synthase	protein	388	39% helix, 16% strand	Q5H1U9
B, C, D	Cystathionine gamma-synthase	protein	387	37% helix, 16% strand	Q5H1U9

Ligands and binding sites

0JO · 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid · ligand · 4 copies · chains A, D, B, C
CYS · Cysteine · ligand · 4 copies · chains A, D, B, C

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	163	0.71	0.89	38	0JO, CYS
2	288	0.69	0.84	59	0JO, CYS
3	290	0.69	0.84	60	0JO, CYS
4	202	0.68	0.86	43	0JO, CYS
5	95	0.56	0.85	31	empty

Interfaces

6 interfaces between chains.

B–C · 2653 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 2637 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 1838 Å² buried · 34 hydrogen bonds · protein-protein
A–C · 1836 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 976 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6LD8 · Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in… · 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 Q5H1U9
Elsewhere: RCSB PDB 6LD8 · PDBe 6LD8 · UniProt Q5H1U9

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