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

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: 6LD9
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: E9U
Pockets: 13 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).

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

Ligands and binding sites

E9U · (2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	388	0.74	0.84	84	E9U
2	216	0.71	0.87	42	E9U
3	191	0.70	0.88	37	E9U
4	283	0.70	0.84	55	E9U
5	171	0.61	0.83	45	empty

Interfaces

6 interfaces between chains.

C–D · 2673 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2667 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 1822 Å² buried · 36 hydrogen bonds · protein-protein
A–C · 1821 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 980 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6LD9 · 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 6LD9 · PDBe 6LD9 · UniProt Q5H1U9

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