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Crystal structure of Mycobacterium smegmatis LmcA with xenon

Analyse Crystal structure of Mycobacterium smegmatis LmcA with xenon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SHW
Type: protein
Length: 513 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.79
Source: Mycolicibacterium smegmatis
Molecule: LmcA
UniProt: A0A653FIR1
Ligands: XE
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · resolution 1.79 · 2 distinct chains · 10% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LmcA	protein	254	10% helix, 51% strand	A0A653FIR1
B	LmcA	protein	259	10% helix, 51% strand	A0A653FIR1

Ligands and binding sites

XE · Xenon · ion · 5 copies · chains A, B
GOL · Glycerol · additive · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	373	0.82	0.91	53	XE
2	439	0.81	0.89	60	XE
3	909	0.77	0.80	68	empty
4	103	0.43	0.78	21	empty

Interfaces

1 interface between chains.

A–B · 678 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7SHW · Crystal structure of mycobacterium smegmatis lmca with xenon · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A653FIR1
Elsewhere: RCSB PDB 7SHW · PDBe 7SHW · UniProt A0A653FIR1

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