MolNFT v1 · #4107 · protein

Structure of the dnag catalytic core

1DD9 · DNA primase: “Structure of the dnag catalytic core”. X-ray diffraction, 1 ligand (SR), 3 pockets (best druggability 0.34). MolNFT v1 #4107 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1DD9
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: SR
Pockets: 3 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA primase (EC 2.7.7.-)	protein	310	50% helix, 16% strand	P0ABS5

Ligands and binding sites

SR · Strontium ion · metal · 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	52	0.34	0.79	13	SR
2	58	0.31	0.76	14	empty
3	71	0.31	0.74	17	empty

Compared structures

1DD9 · 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 1DD9 · PDBe 1DD9 · UniProt P0ABS5

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