MolNFT v1 · #155618 · protein

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

6LD9 · Cystathionine gamma-synthase: “Crystal structure of cystathionine gamma synthase from xanthomonas oryzae pv. oryzae in complex with…”. X-ray diffraction, 1 ligand (E9U), 13 pockets (best druggability 0.74). MolNFT v1 #155618 on…

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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