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Rck domain with cda

Analyse Rck domain with cda in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YS2
Type: protein
Length: 144 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NA+/H+ antiporter-like protein
UniProt: W8TQN9
Ligands: 2BA
Pockets: 1 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	NA+/H+ antiporter-like protein	protein	72	25% helix, 29% strand	W8TQN9

Ligands and binding sites

2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · chains A, 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	220	0.55	0.78	19	2BA

Interfaces

1 interface between chains.

A–B · 566 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (engineered).

Compared structures

4YS2 · RCK domain with CDA · the same entry in another collection · chain A 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 W8TQN9
Elsewhere: RCSB PDB 4YS2 · PDBe 4YS2 · UniProt W8TQN9

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