Research workbench

E. COLI sliding clamp in complex with acqldla

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

PDB: 4K3R
Type: protein
Length: 721 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase III subunit beta; (ACE)QLDLA
EC: 2.7.7.7
UniProt: P0A988
Ligands: ACE, CA, CL
Pockets: 6 · best druggability 0.41

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	358	23% helix, 44% strand	P0A988
B	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	358	23% helix, 46% strand	P0A988
E	(ACE)QLDLA	protein	5	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, E
CA · Calcium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · chains A
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
PGE · Triethylene glycol · additive · chains A
PG4 · Tetraethylene glycol · 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	61	0.41	0.81	18	empty
2	62	0.30	0.75	18	empty
3	73	0.30	0.73	19	empty
4	64	0.28	0.73	18	PG4
5	50	0.27	0.75	13	empty

Interfaces

2 interfaces between chains.

A–B · 1319 Å² buried · 34 hydrogen bonds · protein-protein
A–E · 435 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4K3R · E. coli sliding clamp in complex with AcQLDLA · 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 4K3R · PDBe 4K3R · UniProt P0A988

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