MolNFT v1 · #146455 · protein

Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain Y397L mutant

6DI2: “Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain Y397L mutant”. X-ray diffraction, 1 ligand (SF4), 2 pockets (best druggability 0.58). MolNFT v1 #146455 on GenesisL1: 3D structure, binding sites…

PDB: 6DI2
Type: protein
Length: 183 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primase large subunit
EC: 2.7.7.-
UniProt: C7GP29
Ligands: SF4
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 64% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA primase large subunit (EC 2.7.7.-)	protein	183	64% helix, 0% strand	C7GP29

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.58	0.86	24	SF4, MPD
2	67	0.33	0.76	19	empty

Compared structures

6DI2 · Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain… · the same entry in another collection · chain A against A, TM-score 1.00

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 C7GP29
Elsewhere: RCSB PDB 6DI2 · PDBe 6DI2 · UniProt C7GP29

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