MolNFT v1 · #135840 · protein

XAC2383 from xanthomonas citri bound to chloride ion

5UB3 · Phosphate-binding protein: “XAC2383 from xanthomonas citri bound to chloride ion”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.69). MolNFT v1 #135840 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5UB3
Type: protein
Length: 557 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphate-binding protein
UniProt: Q8PJZ4
Ligands: CL
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphate-binding protein	protein	278	42% helix, 25% strand	Q8PJZ4
B	Phosphate-binding protein	protein	279	43% helix, 25% strand	Q8PJZ4

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, B

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

Pockets

5 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	367	0.69	0.82	38	CL
2	326	0.62	0.79	33	CL
3	86	0.50	0.83	20	CL
4	63	0.40	0.80	18	empty
5	59	0.33	0.76	12	empty

Interfaces

1 interface between chains.

A–B · 347 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5UB3 · XAC2383 from Xanthomonas citri bound to chloride ion · 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 Q8PJZ4
Elsewhere: RCSB PDB 5UB3 · PDBe 5UB3 · UniProt Q8PJZ4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.