MolNFT v1 · #155730 · protein

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

6LGO · Cystathionine gamma-synthase: “Crystal structure of cystathionine gamma synthase from xanthomonas oryzae pv. oryzae in complex with…”. X-ray diffraction, 1 ligand (EBO), 12 pockets (best druggability 0.72). MolNFT v1 #155730 on…

PDB: 6LGO
Type: protein
Length: 1,548 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cystathionine gamma-synthase
UniProt: Q5H1U9
Ligands: EBO
Pockets: 12 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).

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

Ligands and binding sites

EBO · (2~{S})-2-azanyl-4-[(3~{S})-3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonomethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-4-oxidanylidene-butyl]sulfanyl-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

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	305	0.72	0.85	55	EBO
2	199	0.71	0.88	41	EBO
3	289	0.71	0.85	59	EBO
4	227	0.71	0.87	44	EBO
5	154	0.44	0.75	31	empty

Interfaces

6 interfaces between chains.

A–B · 2686 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 2652 Å² buried · 29 hydrogen bonds · protein-protein
A–D · 1835 Å² buried · 33 hydrogen bonds · protein-protein
B–C · 1815 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 997 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6LGO · 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 6LGO · PDBe 6LGO · UniProt Q5H1U9

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