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Crystal structure of S202G mutant of human syt-5 C2A domain

Analyse Crystal structure of S202G mutant of human syt-5 C2A domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5H4Z
Type: protein
Length: 257 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Synaptotagmin-5
UniProt: O00445
Ligands: CA, CL
Pockets: 1 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Synaptotagmin-5	protein	129	2% helix, 52% strand	O00445
B	Synaptotagmin-5	protein	128	5% helix, 52% strand	O00445

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, B
CL · Chloride ion · ion · chains B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	204	0.47	0.74	33	empty

Interfaces

1 interface between chains.

A–B · 531 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5H4Z · Crystal structure of S202G mutant of human SYT-5 C2A domain · the same entry in another collection · chain A against A, TM-score 1.00
O00445 · AlphaFold monomer V2.0 prediction for synaptotagmin-5 (O00445) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 O00445
Elsewhere: RCSB PDB 5H4Z · PDBe 5H4Z · UniProt O00445

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