MolNFT v1 · #23502 · protein

Crystal structure of selenomonas ruminantium phytase complexed with persulfated phytate in the C2221 crystal form

1U25 · Myo-inositol hexaphosphate phosphohydrolase: “Crystal structure of selenomonas ruminantium phytase complexed with persulfated phytate in the C2221 crystal…”. X-ray diffraction, 1 ligand (IHS), 7 pockets (best druggability 0.78).…

PDB: 1U25
Type: protein
Length: 933 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myo-inositol hexaphosphate phosphohydrolase
EC: 3.1.3.72
UniProt: Q7WUJ1
Ligands: IHS
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Myo-inositol hexaphosphate phosphohydrolase (EC 3.1.3.72)	protein	311	37% helix, 17% strand	Q7WUJ1
B	Myo-inositol hexaphosphate phosphohydrolase (EC 3.1.3.72)	protein	312	38% helix, 17% strand	Q7WUJ1
C	Myo-inositol hexaphosphate phosphohydrolase (EC 3.1.3.72)	protein	310	37% helix, 18% strand	Q7WUJ1

Ligands and binding sites

IHS · D-myo-inositol-hexasulphate · ligand · 3 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1101	0.78	0.80	114	IHS
2	796	0.71	0.77	92	empty
3	321	0.55	0.75	50	empty
4	123	0.52	0.82	24	empty
5	128	0.48	0.79	25	empty

Interfaces

2 interfaces between chains.

A–C · 477 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 457 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

1U25 · Crystal structure of Selenomonas ruminantium phytase complexed with persulfated phytate… · 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 Q7WUJ1
Elsewhere: RCSB PDB 1U25 · PDBe 1U25 · UniProt Q7WUJ1

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