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Structure and protein design of human apyrase

Analyse Structure and protein design of human apyrase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1S1D
Type: protein
Length: 632 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apyrase
EC: 3.6.1.5
UniProt: Q8WVQ1
Ligands: GP2, CA, SO4
Pockets: 10 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apyrase (EC 3.6.1.5)	protein	317	7% helix, 52% strand	Q8WVQ1
B	Apyrase (EC 3.6.1.5)	protein	315	7% helix, 52% strand	Q8WVQ1

Ligands and binding sites

GP2 · Phosphomethylphosphonic acid guanosyl ester · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 7 copies · chains A, B
ACT · Acetate ion · additive · chains A

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

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	420	0.82	0.90	41	TRS
2	181	0.71	0.89	24	empty
3	344	0.65	0.80	28	GP2
4	262	0.64	0.82	31	TRS
5	252	0.64	0.82	30	TRS

Interfaces

1 interface between chains.

A–B · 817 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1S1D · Structure and protein design of human apyrase · the same entry in another collection · chain A against A, TM-score 1.00
Q8WVQ1 · AlphaFold monomer V2.0 prediction for soluble calcium-activated nucleotidase 1 (Q8WVQ1) · a predicted model of the same protein · chain B 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 Q8WVQ1
Elsewhere: RCSB PDB 1S1D · PDBe 1S1D · UniProt Q8WVQ1

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