Research workbench

Crystal structure of prib binary complex with product diphosphate

Analyse Crystal structure of prib binary complex with product diphosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K9M
Type: protein
Length: 353 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prib prenyltransferase
Ligands: POP
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prib prenyltransferase	protein	353	39% helix, 22% strand	—

Ligands and binding sites

POP · Pyrophosphate 2- · ligand · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

2 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	217	0.78	0.92	37	POP, TRS
2	175	0.56	0.81	36	empty

Compared structures

5K9M · Crystal Structure of PriB Binary Complex with Product Diphosphate · 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
Elsewhere: RCSB PDB 5K9M · PDBe 5K9M

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