MolNFT v1 · #123627 · protein

Yersinia pestis dhps with pterine-sulfa conjugate compound 16

5JQ9 · Dihydropteroate synthase: “Yersinia pestis dhps with pterine-sulfa conjugate compound 16”. X-ray diffraction, 1 ligand (6MB), 4 pockets (best druggability 0.70). MolNFT v1 #123627 on GenesisL1: 3D structure, binding sites and…

PDB: 5JQ9
Type: protein
Length: 509 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydropteroate synthase
EC: 2.5.1.15
UniProt: A0A0J9WZK8
Ligands: 6MB
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dihydropteroate synthase (EC 2.5.1.15)	protein	257	49% helix, 18% strand	A0A0J9WZK8
B	Dihydropteroate synthase (EC 2.5.1.15)	protein	252	50% helix, 18% strand	A0A0J9WZK8

Ligands and binding sites

6MB · 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl) methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	105	0.70	0.93	38	empty
2	194	0.55	0.80	28	6MB
3	148	0.54	0.81	32	6MB
4	63	0.30	0.74	11	empty

Interfaces

1 interface between chains.

A–B · 1101 Å² buried · 0 hydrogen bonds · protein-protein

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 A0A0J9WZK8
Elsewhere: RCSB PDB 5JQ9 · PDBe 5JQ9 · UniProt A0A0J9WZK8

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