MolNFT v1 · #114934 · protein

APH(2")-iva in complex with get (G418) at room temperature

5C4K · APH(2'')-id: “APH(2")-iva in complex with get (G418) at room temperature”. X-ray diffraction, 1 ligand (GET), 7 pockets (best druggability 0.76). MolNFT v1 #114934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5C4K
Type: protein
Length: 593 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: APH(2'')-id
UniProt: O68183
Ligands: GET
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	APH(2'')-id	protein	296	50% helix, 16% strand	O68183
B	APH(2'')-id	protein	297	50% helix, 15% strand	O68183

Ligands and binding sites

GET · Geneticin · ligand · chains A

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1080	0.76	0.78	76	empty
2	1103	0.76	0.78	74	GET
3	54	0.34	0.78	12	empty
4	77	0.34	0.75	14	empty
5	83	0.31	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 72 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5C4K · APH(2")-IVa in complex with GET (G418) at room temperature · 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 O68183
Elsewhere: RCSB PDB 5C4K · PDBe 5C4K · UniProt O68183

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