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Crystal structure of human AP4A hydrolase

Analyse Crystal structure of human AP4A hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3U53
Type: protein
Length: 576 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BIS(5'-nucleosyl)-tetraphosphatase [asymmetrical]
EC: 3.6.1.17
UniProt: P50583
Ligands: SO4
Pockets: 5 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	BIS(5'-nucleosyl)-tetraphosphatase [asymmetrical] (EC 3.6.1.17)	protein	144	29% helix, 39% strand	P50583

Ligands and binding sites

SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D
GOL · Glycerol · additive · chains A

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	151	0.46	0.77	28	SO4
2	163	0.45	0.76	25	SO4
3	148	0.41	0.74	26	SO4
4	92	0.35	0.75	21	SO4
5	56	0.28	0.74	15	empty

Interfaces

4 interfaces between chains.

A–D · 759 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 634 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 68 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 38 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3U53 · Crystal structure of human Ap4A hydrolase · the same entry in another collection · chain D against D, TM-score 1.00
P50583 · AlphaFold monomer V2.0 prediction for BIS(5'-nucleosyl)-tetraphosphatase [asymmetrical]… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P50583
Elsewhere: RCSB PDB 3U53 · PDBe 3U53 · UniProt P50583

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