MolNFT v2 · #216513 · protein

Sub-tomogram average of the Nap adhesion complex from the human pathogen Mycoplasma genitalium at 11 Angstrom.

8PBZ · Mgp-operon protein 3: “Sub-tomogram average of the Nap adhesion complex from the human pathogen Mycoplasma genitalium at 11 Angstrom.”. Electron microscopy at 11.0, 3 ligands (BGC, GAL, SIA), 20 pockets (best druggability 0.88).…

PDB: 8PBZ
Type: protein
Length: 4,766 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 11.0
Source: Mycoplasmoides genitalium G37
Molecule: Mgp-operon protein 3; Adhesin P1
UniProt: P22747, P20796
Ligands: BGC, GAL, SIA
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 11.0 · 2 distinct chains · 22% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Mgp-operon protein 3	protein	1003	22% helix, 29% strand	P22747
B, E	Adhesin P1	protein	1380	22% helix, 19% strand	P20796

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B, D, E
GAL · beta-D-galactopyranose · sugar · 2 copies
SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B, D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	925	0.88	0.90	124	empty
2	676	0.82	0.86	93	empty
3	409	0.80	0.89	47	empty
4	960	0.80	0.82	87	empty
5	925	0.79	0.81	89	empty

Interfaces

6 interfaces between chains.

A–B · 3530 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 3487 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 3041 Å² buried · 47 hydrogen bonds · protein-protein
A–E · 2931 Å² buried · 41 hydrogen bonds · protein-protein
B–E · 422 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

P20796 · AlphaFold monomer V2.0 prediction for adhesin P1 (P20796) · a predicted model of the same protein · chain E against A, TM-score 0.92
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 0.89

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 P22747
Every structure of UniProt P20796
Elsewhere: RCSB PDB 8PBZ · PDBe 8PBZ · UniProt P22747 · UniProt P20796

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