Research workbench

E. COLI sliding clamp in complex with 3,4-difluorobenzamide

Analyse E. COLI sliding clamp in complex with 3,4-difluorobenzamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4N94
Type: protein
Length: 725 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase III subunit beta
EC: 2.7.7.7
UniProt: P0A988
Ligands: 2HO, CA, CL
Pockets: 6 · best druggability 0.35

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	360	22% helix, 48% strand	P0A988
B	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	365	21% helix, 46% strand	P0A988

Ligands and binding sites

2HO · 3,4-difluorobenzamide · ligand · chains A
CA · Calcium ion · metal · 2 copies · chains B
CL · Chloride ion · ion · chains A
PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains B
EDO · 1,2-ethanediol · additive · chains B

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

Pockets

6 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	88	0.35	0.75	18	empty
2	101	0.35	0.74	22	empty
3	54	0.31	0.77	14	empty
4	65	0.29	0.74	18	empty
5	64	0.29	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 1304 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

4N94 · E. coli sliding clamp in complex with 3,4-difluorobenzamide · the same entry in another collection · chain B against B, 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 0.99

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 P0A988
Elsewhere: RCSB PDB 4N94 · PDBe 4N94 · UniProt P0A988

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