MolNFT v1 · #98741 · protein

Crystal structure of the catalytic subunit of human primase

4LIK · DNA primase small subunit: “Crystal structure of the catalytic subunit of human primase”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.62). MolNFT v1 #98741 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4LIK
Type: protein
Length: 369 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: P49642
Ligands: ZN
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA primase small subunit (EC 2.7.7.-)	protein	369	50% helix, 12% strand	P49642

Ligands and binding sites

ZN · Zinc ion · metal · chains A
CIT · Citric acid · additive · 3 copies · chains A

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

Pockets

7 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	102	0.62	0.88	22	empty
2	94	0.46	0.80	16	empty
3	55	0.38	0.80	17	empty
4	115	0.36	0.73	20	CIT
5	56	0.32	0.76	14	empty

Compared structures

4LIK · Crystal structure of the catalytic subunit of human primase · the same entry in another collection · chain A against A, TM-score 1.00
P49642 · AlphaFold monomer V2.0 prediction for DNA primase small subunit (P49642) · 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 P49642
Elsewhere: RCSB PDB 4LIK · PDBe 4LIK · UniProt P49642

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