MolNFT v1 · #55313 · protein

Complex of cambr and cam

2YGG · SODIUM/HYDROGEN exchanger 1: “Complex of cambr and cam”. X-ray diffraction, 2 ligands (TAM, CA), 3 pockets (best druggability 0.36). MolNFT v1 #55313 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YGG
Type: protein
Length: 212 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SODIUM/HYDROGEN exchanger 1; Calmodulin
UniProt: P19634, P62161
Ligands: TAM, CA
Pockets: 3 · best druggability 0.36

Structure

x-ray diffraction · 2 distinct chains · 67% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SODIUM/HYDROGEN exchanger 1	protein	66	77% helix, 0% strand	P19634
B	Calmodulin	protein	146	63% helix, 5% strand	P62161

Ligands and binding sites

TAM · Tris(hydroxyethyl)aminomethane · ligand · 3 copies · chains A, B
CA · Calcium ion · metal · 4 copies · chains B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B

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

Pockets

3 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	106	0.36	0.74	20	empty
2	74	0.36	0.76	11	MRD
3	62	0.28	0.73	15	empty

Interfaces

1 interface between chains.

A–B · 1233 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

2YGG · Complex of CaMBR and CaM · the same entry in another collection · chain A against A, TM-score 1.00
P19634 · AlphaFold monomer V2.0 prediction for SODIUM/HYDROGEN exchanger 1 (P19634) · a predicted model of the same protein · chain A against A, TM-score 0.47

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 P19634
Every structure of UniProt P62161
Elsewhere: RCSB PDB 2YGG · PDBe 2YGG · UniProt P19634 · UniProt P62161

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.