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The structure of the S. aureus dnag RNA polymerase domain

Analyse The structure of the S. aureus dnag RNA polymerase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4E2K
Type: protein
Length: 319 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primase
EC: 2.7.7.-
UniProt: O05338
Ligands: BEN
Pockets: 5 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA primase (EC 2.7.7.-)	protein	319	54% helix, 14% strand	O05338

Ligands and binding sites

BEN · Benzamidine · ligand · 2 copies · chains A

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

Pockets

5 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	62	0.46	0.83	13	empty
2	120	0.42	0.76	23	empty
3	108	0.39	0.75	21	empty
4	54	0.34	0.78	11	empty
5	50	0.30	0.76	13	empty

Compared structures

4E2K · The structure of the S. aureus DnaG RNA Polymerase Domain · the same entry in another collection · chain A against A, TM-score 1.00
O05338 · AlphaFold monomer V2.0 prediction for DNA primase (O05338) · 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 O05338
Elsewhere: RCSB PDB 4E2K · PDBe 4E2K · UniProt O05338

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