MolNFT v1 · #162742 · protein

Crystal structure of mouse CD11B I-domain (CD11B-I) in complex with staphylococcus aureus octameric bi-component leukocidin lukgh (lukh K319A mutant)

6RHV · Beta-channel forming cytolysin: “Crystal structure of mouse CD11B I-domain (CD11B-I) in complex with staphylococcus aureus octameric…”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.78). MolNFT v1 #162742 on…

PDB: 6RHV
Type: protein
Length: 741 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-channel forming cytolysin; Integrin alpha-M
UniProt: A0A0D6HCK9, A0A0D6HC73, P05555
Ligands: MG
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Beta-channel forming cytolysin	protein	283	4% helix, 61% strand	A0A0D6HCK9
H	Beta-channel forming cytolysin	protein	288	4% helix, 58% strand	A0A0D6HC73
C	Integrin alpha-M	protein	170	39% helix, 24% strand	P05555

Ligands and binding sites

MG · Magnesium ion · metal · chains H, C
DMS · Dimethyl sulfoxide · additive · 6 copies · chains G, H, C

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

Pockets

6 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	1040	0.78	0.80	87	DMS
2	436	0.72	0.83	49	DMS
3	95	0.45	0.80	25	empty
4	60	0.35	0.78	16	empty
5	93	0.34	0.74	17	empty

Interfaces

3 interfaces between chains.

G–H · 2335 Å² buried · 63 hydrogen bonds · protein-protein
H–C · 810 Å² buried · 24 hydrogen bonds · protein-protein
G–C · 404 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6RHV · Crystal structure of mouse CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus… · the same entry in another collection · chain G against G, TM-score 1.00
P05555 · AlphaFold monomer V2.0 prediction for integrin alpha-M (P05555) · a predicted model of the same protein · chain C 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 A0A0D6HCK9
Every structure of UniProt A0A0D6HC73
Every structure of UniProt P05555
Elsewhere: RCSB PDB 6RHV · PDBe 6RHV · UniProt A0A0D6HCK9 · UniProt A0A0D6HC73 · UniProt P05555

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.