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Sub-tomogram average of the closed conformation of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.

Analyse Sub-tomogram average of the closed conformation of the Nap adhesion complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8PC1
Type: protein
Length: 2,187 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 18.0
Source: Mycoplasmoides genitalium G37
Molecule: Adhesin P1; Mgp-operon protein 3
UniProt: P20796, P22747
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · resolution 18.0 · 2 distinct chains · 17% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Adhesin P1	protein	1285	18% helix, 20% strand	P20796
A	Mgp-operon protein 3	protein	902	16% helix, 30% strand	P22747

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	951	0.83	0.84	94	empty
2	280	0.81	0.92	39	empty
3	995	0.78	0.80	90	empty
4	826	0.76	0.80	72	empty
5	113	0.76	0.96	32	empty

Interfaces

1 interface between chains.

B–A · 3629 Å² buried · 47 hydrogen bonds · protein-protein

Compared structures

P22747 · AlphaFold monomer V2.0 prediction for mgp-operon protein 3 (P22747) · a predicted model of the same protein · chain A against A, TM-score 0.99
P20796 · AlphaFold monomer V2.0 prediction for adhesin P1 (P20796) · 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 P20796
Every structure of UniProt P22747
Elsewhere: RCSB PDB 8PC1 · PDBe 8PC1 · UniProt P20796 · UniProt P22747

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