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Crystal structure of human CD11B I-domain (CD11B-I) in complex with staphylococcus aureus octameric bi-component leukocidin lukgh

Analyse Crystal structure of human CD11B I-domain (CD11B-I) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RHW
Type: protein
Length: 711 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, P11215
Ligands: MG
Pockets: 5 · best druggability 0.77

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	272	4% helix, 59% strand	A0A0D6HCK9
H	Beta-channel forming cytolysin	protein	271	4% helix, 60% strand	A0A0D6HC73
C	Integrin alpha-M	protein	168	36% helix, 24% strand	P11215

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

5 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	1167	0.77	0.79	90	DMS
2	595	0.72	0.80	65	DMS
3	55	0.32	0.75	10	empty
4	62	0.31	0.74	13	empty
5	71	0.28	0.72	18	empty

Interfaces

3 interfaces between chains.

G–H · 1984 Å² buried · 54 hydrogen bonds · protein-protein
H–C · 784 Å² buried · 28 hydrogen bonds · protein-protein
G–C · 275 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6RHW · Crystal structure of human CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus… · the same entry in another collection · chain G against G, TM-score 1.00
P11215 · AlphaFold monomer V2.0 prediction for integrin alpha-M (P11215) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 P11215
Elsewhere: RCSB PDB 6RHW · PDBe 6RHW · UniProt A0A0D6HCK9 · UniProt A0A0D6HC73 · UniProt P11215

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