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The crystal structure of human synapsin III (SYN3) in complex with amppnp

Analyse The crystal structure of human synapsin III (SYN3) in complex with amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P0A
Type: protein
Length: 596 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Synapsin-3
UniProt: O14994
Ligands: ANP, SO4, CL
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Synapsin-3	protein	298	30% helix, 33% strand	O14994

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 8 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	348	0.81	0.90	58	SO4, ANP
2	481	0.78	0.86	76	CL, SO4, ANP
3	396	0.64	0.78	55	SO4
4	182	0.44	0.74	33	empty
5	104	0.39	0.76	21	CL, SO4, EDO

Interfaces

1 interface between chains.

A–B · 1746 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

2P0A · The crystal structure of human synapsin III (SYN3) in complex with AMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
O14994 · AlphaFold monomer V2.0 prediction for synapsin-3 (O14994) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O14994
Elsewhere: RCSB PDB 2P0A · PDBe 2P0A · UniProt O14994

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