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Crystal structure of AMYK38 with rubidium ion

Analyse Crystal structure of AMYK38 with rubidium ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1UD5
Type: protein
Length: 480 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amylase
EC: 3.2.1.1
UniProt: Q93I48
Ligands: RB, NA
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Amylase (EC 3.2.1.1)	protein	480	26% helix, 27% strand	Q93I48

Ligands and binding sites

RB · Rubidium ion · metal · 6 copies · chains A
NA · Sodium ion · metal · 2 copies · chains A

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	156	0.49	0.78	24	empty
2	66	0.37	0.78	14	empty
3	53	0.25	0.73	21	empty

Compared structures

1UD5 · Crystal structure of AmyK38 with rubidium ion · 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 Q93I48
Elsewhere: RCSB PDB 1UD5 · PDBe 1UD5 · UniProt Q93I48

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