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Crystal structure of the C2B domain of trypanosoma brucei extended synaptotagmin (E-syt)

Analyse Crystal structure of the C2B domain of trypanosoma brucei extended… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7A1R
Type: protein
Length: 242 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Synaptotagmin
UniProt: A0A3L6KWL9
Ligands: CA, NA, CL
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Synaptotagmin	protein	121	7% helix, 55% strand	A0A3L6KWL9

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 7 copies · chains A, B
ACT · Acetate ion · additive · chains B

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

Pockets

2 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	126	0.45	0.77	18	CL
2	119	0.43	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 580 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7A1R · Crystal structure of the C2B domain of Trypanosoma brucei extended synaptotagmin (E-Syt) · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt A0A3L6KWL9
Elsewhere: RCSB PDB 7A1R · PDBe 7A1R · UniProt A0A3L6KWL9

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