MolNFT v1 · #135841 · protein

XAC2383 from xanthomonas citri bound to phosphate

5UB4 · Phosphate-binding protein: “XAC2383 from xanthomonas citri bound to phosphate”. X-ray diffraction, 2 ligands (CL, PO4), 6 pockets (best druggability 0.68). MolNFT v1 #135841 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5UB4
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, PO4
Pockets: 6 · best druggability 0.68

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	42% helix, 25% strand	Q8PJZ4

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	382	0.68	0.81	36	PO4
2	340	0.64	0.80	34	PO4
3	120	0.47	0.79	25	empty
4	69	0.46	0.83	20	CL
5	54	0.36	0.79	12	empty

Interfaces

1 interface between chains.

A–B · 380 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5UB4 · XAC2383 from Xanthomonas citri bound to phosphate · 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 5UB4 · PDBe 5UB4 · UniProt Q8PJZ4

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