MolNFT v1 · #17989 · protein

Nucleoside diphosphate kinase

1PAE · Nucleoside diphosphate kinase, cytosolic: “Nucleoside diphosphate kinase”. X-ray diffraction, 1 ligand (SE), 1 pocket (best druggability 0.50). MolNFT v1 #17989 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PAE
Type: protein
Length: 148 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase, cytosolic
EC: 2.7.4.6
UniProt: P22887
Ligands: SE
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Nucleoside diphosphate kinase, cytosolic (EC 2.7.4.6)	protein	148	44% helix, 18% strand	P22887

Ligands and binding sites

SE · Selenium atom · ion · 2 copies · chains X

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	173	0.50	0.78	28	SE

Modifications

Observed in the structure: 2 modified (engineered).

Compared structures

1PAE · nucleoside diphosphate kinase · the same entry in another collection · chain X against X, TM-score 1.00
P22887 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase, cytosolic (P22887) · a predicted model of the same protein · chain X against A, TM-score 0.99

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 P22887
Elsewhere: RCSB PDB 1PAE · PDBe 1PAE · UniProt P22887

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