Research workbench

N-domain P40/P90 mycoplasma pneumoniae complexed with 3'SL

Analyse N-domain P40/P90 mycoplasma pneumoniae complexed with 3'SL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TLZ
Type: protein
Length: 1,613 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mgp-operon protein 3
UniProt: Q50341
Ligands: BGC, GAL, SIA
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mgp-operon protein 3	protein	803	13% helix, 29% strand	Q50341
B	Mgp-operon protein 3	protein	810	13% helix, 29% strand	Q50341

Ligands and binding sites

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

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1047	0.82	0.83	90	empty
2	1189	0.79	0.81	104	empty
3	812	0.78	0.82	80	empty
4	170	0.58	0.82	27	empty
5	53	0.58	0.91	20	empty

Interfaces

1 interface between chains.

A–B · 579 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6TLZ · N-Domain P40/P90 Mycoplasma pneumoniae complexed with 3'SL · the same entry in another collection · chain A against A, TM-score 1.00
Q50341 · AlphaFold monomer V2.0 prediction for mgp-operon protein 3 (Q50341) · 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 Q50341
Elsewhere: RCSB PDB 6TLZ · PDBe 6TLZ · UniProt Q50341

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