Research workbench

Structural insights into the unique single-stranded DNA binding mode of DNA processing protein a from helicobacter pylori

Analyse Structural insights into the unique single-stranded DNA binding mode of DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LJR
Type: protein + DNA
Length: 433 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA processing chain a; Single-stranded DNA
UniProt: O25100
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA processing chain a	protein	213	42% helix, 15% strand	O25100
C	Single-stranded DNA	dna	6	—	—
D	Single-stranded DNA	dna	1	—	—

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	113	0.56	0.84	24	empty
2	76	0.53	0.86	21	empty
3	71	0.40	0.79	20	empty

Interfaces

3 interfaces between chains.

A–B · 755 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 550 Å² buried · 8 hydrogen bonds · protein-nucleic
A–D · 250 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

4LJR · Structural insights into the unique single-stranded DNA binding mode of DNA processing… · 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 O25100
Elsewhere: RCSB PDB 4LJR · PDBe 4LJR · UniProt O25100

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.