MolNFT v1 · #18690 · protein

Crystal structure of rat synapsin I C domain complexed to CA.ATP (form 1)

1PX2: “Crystal structure of rat synapsin I C domain complexed to CA.ATP (form 1)”. X-ray diffraction, 2 ligands (ATP, CA), 8 pockets (best druggability 0.78). MolNFT v1 #18690 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PX2
Type: protein
Length: 588 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Synapsin I
UniProt: P09951
Ligands: ATP, CA
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Synapsin I	protein	294	31% helix, 33% strand	P09951
B	Synapsin I	protein	294	30% helix, 33% strand	P09951

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

8 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	598	0.78	0.84	75	CA, ATP
2	512	0.76	0.84	57	CA, ATP
3	589	0.63	0.75	63	empty
4	93	0.37	0.76	19	empty
5	130	0.37	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 1864 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

1PX2 · Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP (Form 1) · the same entry in another collection · chain A against A, TM-score 1.00
P09951 · AlphaFold monomer V2.0 prediction for synapsin-1 (P09951) · 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 P09951
Elsewhere: RCSB PDB 1PX2 · PDBe 1PX2 · UniProt P09951

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