Research workbench

E. COLI sliding clamp in P1 crystal space group

Analyse E. COLI sliding clamp in P1 crystal space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K3S
Type: protein
Length: 724 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: CA
Pockets: 7 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	359	22% helix, 47% strand	P0A988
B	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	365	21% helix, 45% strand	P0A988

Ligands and binding sites

CA · Calcium ion · metal · chains A
PG4 · Tetraethylene glycol · additive · chains B
P4C · O-acetaldehydyl-hexaethylene glycol · additive · chains A, B

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

Pockets

7 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	163	0.44	0.75	26	PG4
2	95	0.36	0.75	17	empty
3	65	0.34	0.76	12	empty
4	72	0.30	0.74	17	empty
5	65	0.29	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 1350 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

4K3S · E. coli sliding clamp in P1 crystal space group · 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 B 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 4K3S · PDBe 4K3S · UniProt P0A988

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