MolNFT v1 · #4109 · protein

Structure of the dnag catalytic core

1DDE · DNA primase: “Structure of the dnag catalytic core”. X-ray diffraction, 1 ligand (Y1), 2 pockets (best druggability 0.35). MolNFT v1 #4109 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1DDE
Type: protein
Length: 310 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primase
EC: 2.7.7.-
UniProt: P0ABS5
Ligands: Y1
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA primase (EC 2.7.7.-)	protein	310	51% helix, 18% strand	P0ABS5

Ligands and binding sites

Y1 · Yttrium ion · metal · 4 copies · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.35	0.78	20	empty
2	75	0.31	0.74	17	empty

Compared structures

1DDE · Structure of the dnag catalytic core · the same entry in another collection · chain A against A, TM-score 1.00
P0ABS5 · AlphaFold monomer V2.0 prediction for DNA primase (P0ABS5) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P0ABS5
Elsewhere: RCSB PDB 1DDE · PDBe 1DDE · UniProt P0ABS5

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