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XAC2383 from xanthomonas citri bound to pyrophosphate

Analyse XAC2383 from xanthomonas citri bound to pyrophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UB6
Type: protein
Length: 558 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphate-binding protein
UniProt: Q8PJZ4
Ligands: POP
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 25% strand (DSSP).

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

Ligands and binding sites

POP · Pyrophosphate 2- · ligand · 2 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	478	0.70	0.80	47	POP
2	338	0.63	0.79	33	POP
3	73	0.49	0.84	19	empty
4	107	0.34	0.73	17	empty
5	53	0.34	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 404 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5UB6 · XAC2383 from Xanthomonas citri bound to pyrophosphate · 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 5UB6 · PDBe 5UB6 · UniProt Q8PJZ4

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