Research workbench

Cryo-EM structure of the Gp168-beta-clamp complex

Analyse Cryo-EM structure of the Gp168-beta-clamp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EVP
Type: protein
Length: 840 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.2
Source: Staphylococcus aureus; Staphylococcus virus Twort
Molecule: Beta sliding clamp; Sliding clamp inhibitor
UniProt: P0A024, A0A6H0X5G8
Pockets: 5 · best druggability 0.72

Structure

electron microscopy · resolution 3.2 · 2 distinct chains · 22% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta sliding clamp	protein	377	16% helix, 36% strand	P0A024
C, D	Sliding clamp inhibitor	protein	43	77% helix, 0% strand	A0A6H0X5G8

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1138	0.72	0.76	87	empty
2	1109	0.72	0.76	91	empty
3	61	0.33	0.76	17	empty
4	54	0.32	0.77	14	empty
5	56	0.29	0.76	15	empty

Interfaces

6 interfaces between chains.

A–B · 1256 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 843 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 527 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 524 Å² buried · 5 hydrogen bonds · protein-protein
C–B · 249 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7EVP · Cryo-EM structure of the GP168-beta-clamp complex · the same entry in another collection · chain A against A, TM-score 1.00
P0A024 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0A024) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P0A024
Every structure of UniProt A0A6H0X5G8
Elsewhere: RCSB PDB 7EVP · PDBe 7EVP · UniProt P0A024 · UniProt A0A6H0X5G8

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