MolNFT v1 · #18297 · protein

Crystal structure of rat synapsin I C domain complexed to CA.ATP

1PK8: “Crystal structure of rat synapsin I C domain complexed to CA.ATP”. X-ray diffraction, 2 ligands (ATP, CA), 20 pockets (best druggability 0.85). MolNFT v1 #18297 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PK8
Type: protein
Length: 2,334 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rat synapsin I
UniProt: P09951
Ligands: ATP, CA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 8 distinct chains · 30% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rat synapsin I	protein	306	28% helix, 34% strand	P09951
B	Rat synapsin I	protein	292	29% helix, 32% strand	P09951
C	Rat synapsin I	protein	285	31% helix, 32% strand	P09951
D	Rat synapsin I	protein	300	28% helix, 32% strand	P09951
E	Rat synapsin I	protein	286	30% helix, 31% strand	P09951
F	Rat synapsin I	protein	286	31% helix, 31% strand	P09951
G	Rat synapsin I	protein	293	30% helix, 32% strand	P09951
H	Rat synapsin I	protein	286	31% helix, 31% strand	P09951

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	919	0.85	0.86	110	empty
2	815	0.83	0.86	93	empty
3	827	0.83	0.85	93	CA, ATP
4	445	0.82	0.89	63	CA, ATP
5	651	0.80	0.85	82	CA, ATP

Interfaces

13 interfaces between chains.

A–B · 1864 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 1820 Å² buried · 31 hydrogen bonds · protein-protein
E–F · 1816 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1815 Å² buried · 29 hydrogen bonds · protein-protein
F–G · 1025 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1PK8 · Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP · the same entry in another collection · chain H against H, TM-score 1.00
P09951 · AlphaFold monomer V2.0 prediction for synapsin-1 (P09951) · a predicted model of the same protein · chain H 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 1PK8 · PDBe 1PK8 · UniProt P09951

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