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E. coli sliding clamp in complex with AcQADLF

Analyse E. coli sliding clamp in complex with AcQADLF in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K3O
Type: protein
Length: 725 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2
Source: Escherichia coli; SYNTHETIC CONSTRUCT
Molecule: DNA polymerase III subunit beta; (ACE)QADLF
EC: 2.7.7.7
UniProt: P0A988
Ligands: CA
Pockets: 3 · best druggability 0.30

Structure

x-ray diffraction · resolution 2 · 3 distinct chains · 22% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	360	23% helix, 44% strand	P0A988
B	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	360	23% helix, 46% strand	P0A988
E	(ACE)QADLF	protein	5	0% helix, 0% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
PGE · Triethylene glycol · additive · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 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	66	0.30	0.74	16	empty
2	61	0.29	0.74	15	CA, PG4
3	51	0.26	0.74	17	PEG

Interfaces

2 interfaces between chains.

A–B · 1326 Å² buried · 34 hydrogen bonds · protein-protein
A–E · 448 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4K3O · E. COLI sliding clamp in complex with acqadlf · the same entry in another collection · chain A against A, TM-score 1.00
P0A988 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0A988) · a predicted model of the same protein · chain A 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 P0A988
Elsewhere: RCSB PDB 4K3O · PDBe 4K3O · UniProt P0A988

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