MolNFT v1 · #135844 · protein

XAC2383 from xanthomonas citri bound to ATP

5UB7 · Phosphate-binding protein: “XAC2383 from xanthomonas citri bound to ATP”. X-ray diffraction, 1 ligand (ATP), 6 pockets (best druggability 0.66). MolNFT v1 #135844 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5UB7
Type: protein
Length: 553 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphate-binding protein
UniProt: Q8PJZ4
Ligands: ATP
Pockets: 6 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 26% 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	275	41% helix, 27% strand	Q8PJZ4

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 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	321	0.66	0.81	33	ATP
2	328	0.59	0.77	30	ATP
3	84	0.48	0.82	19	empty
4	111	0.37	0.74	17	empty
5	52	0.35	0.79	12	empty

Interfaces

1 interface between chains.

A–B · 455 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5UB7 · XAC2383 from Xanthomonas citri bound to ATP · 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 5UB7 · PDBe 5UB7 · UniProt Q8PJZ4

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