Research workbench

Bacillus subtilis DNA clamp loader delta protein (yqen)

Analyse Bacillus subtilis DNA clamp loader delta protein (yqen) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZH9
Type: protein
Length: 339 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Delta
EC: 2.7.7.7
UniProt: P54459
Ligands: SO4
Pockets: 3 · best druggability 0.41

Structure

x-ray diffraction · 1 distinct chain · 60% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Delta (EC 2.7.7.7)	protein	339	60% helix, 9% strand	P54459

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains B
GOL · Glycerol · additive · 7 copies · chains B

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	50	0.41	0.83	16	SO4
2	72	0.39	0.78	13	empty
3	51	0.27	0.74	14	empty

Compared structures

3ZH9 · Bacillus subtilis DNA clamp loader delta protein (YqeN) · the same entry in another collection · chain B against B, TM-score 1.00
P54459 · AlphaFold monomer V2.0 prediction for uncharacterized protein yqen (P54459) · a predicted model of the same protein · chain B 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 P54459
Elsewhere: RCSB PDB 3ZH9 · PDBe 3ZH9 · UniProt P54459

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