MolNFT v1 · #24686 · protein

Crystal structure of pyrococcus horikoshii DNA primase-UTP complex

1V34 · DNA primase small subunit: “Crystal structure of pyrococcus horikoshii DNA primase-UTP complex”. X-ray diffraction, 2 ligands (UTP, ZN), 3 pockets (best druggability 0.52). MolNFT v1 #24686 on GenesisL1: 3D structure, binding sites…

PDB: 1V34
Type: protein
Length: 346 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primase small subunit
EC: 2.7.7.-
UniProt: O57934
Ligands: UTP, ZN
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA primase small subunit (EC 2.7.7.-)	protein	346	49% helix, 13% strand	O57934

Ligands and binding sites

UTP · Uridine 5'-triphosphate · ligand · chains A
ZN · Zinc 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	172	0.52	0.79	24	UTP
2	79	0.39	0.78	18	empty
3	68	0.28	0.72	15	empty

Compared structures

1V34 · Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex · the same entry in another collection · chain A against A, TM-score 1.00
O57934 · AlphaFold monomer V2.0 prediction for DNA primase small subunit pris (O57934) · a predicted model of the same protein · chain A 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 O57934
Elsewhere: RCSB PDB 1V34 · PDBe 1V34 · UniProt O57934

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