MolNFT v1 · #99971 · protein

E. COLI sliding clamp in complex with (R)-vedaprofen

4MJP · DNA polymerase III subunit beta: “E. COLI sliding clamp in complex with (R)-vedaprofen”. X-ray diffraction, 3 ligands (27O, CA, CL), 7 pockets (best druggability 0.42). MolNFT v1 #99971 on GenesisL1: 3D structure, binding sites and…

PDB: 4MJP
Type: protein
Length: 720 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: 27O, CA, CL
Pockets: 7 · best druggability 0.42

Structure

x-ray diffraction · 2 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	361	23% helix, 43% strand	P0A988
B	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	359	23% helix, 47% strand	P0A988

Ligands and binding sites

27O · (2R)-2-(4-cyclohexylnaphthalen-1-yl)propanoic acid · ligand · chains B
CA · Calcium ion · metal · chains A
CL · Chloride ion · ion · 3 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
PGE · Triethylene glycol · additive · 2 copies · 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	102	0.42	0.77	19	PEG
2	67	0.37	0.78	14	27O
3	70	0.32	0.75	17	empty
4	72	0.31	0.74	18	PGE
5	63	0.29	0.74	18	CL

Interfaces

1 interface between chains.

A–B · 1331 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

4MJP · E. coli sliding clamp in complex with (R)-Vedaprofen · 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 4MJP · PDBe 4MJP · UniProt P0A988

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