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Structure of a small molecule inhibitor bound to a DNA sliding clamp

Analyse Structure of a small molecule inhibitor bound to a DNA sliding clamp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3D1G
Type: protein
Length: 732 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: 322
Pockets: 9 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	366	22% helix, 46% strand	P0A988

Ligands and binding sites

322 · [(5R)-5-(2,3-dibromo-5-ethoxy-4-hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid · ligand · 2 copies · chains A, B

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

Pockets

9 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	154	0.43	0.75	29	empty
2	92	0.39	0.77	16	empty
3	57	0.33	0.77	17	322
4	65	0.32	0.75	13	empty
5	73	0.32	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 1352 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

3D1G · Structure of a small molecule inhibitor bound to a DNA sliding clamp · 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 0.99

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 3D1G · PDBe 3D1G · UniProt P0A988

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