Research workbench

Ncs-1 bound to a ligand

Analyse Ncs-1 bound to a ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QI4
Type: protein
Length: 373 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuronal calcium sensor 1
UniProt: P62166
Ligands: FKW, CA, NA
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Neuronal calcium sensor 1	protein	187	64% helix, 5% strand	P62166
C	Neuronal calcium sensor 1	protein	186	63% helix, 4% strand	P62166

Ligands and binding sites

FKW · 2-(1~{H}-indol-3-yl)-~{N}-[(~{E})-(4-nitro-3-oxidanyl-phenyl)methylideneamino]ethanamide · ligand · chains B
CA · Calcium ion · metal · 6 copies · chains B, C
NA · Sodium ion · metal · 2 copies · chains B, C
1PE · Pentaethylene glycol · additive · 5 copies · chains B, C
P6G · Hexaethylene glycol · additive · 2 copies · chains B, C
DMS · Dimethyl sulfoxide · additive · chains B
ACT · Acetate ion · additive · chains B

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

Pockets

5 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	814	0.72	0.78	56	ACT
2	659	0.69	0.76	49	P6G, 1PE
3	585	0.66	0.76	47	1PE, FKW
4	152	0.40	0.73	23	empty
5	56	0.32	0.76	17	empty

Interfaces

1 interface between chains.

B–C · 289 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6QI4 · NCS-1 bound to a ligand · the same entry in another collection · chain C against C, TM-score 1.00
P62166 · AlphaFold monomer V2.0 prediction for neuronal calcium sensor 1 (P62166) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P62166
Elsewhere: RCSB PDB 6QI4 · PDBe 6QI4 · UniProt P62166

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