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Mycoplasma arthritidis-derived mitogen complexed with class II MHC molecule HLA-DR1/HA complex in the presence of edta

Analyse Mycoplasma arthritidis-derived mitogen complexed with class II MHC molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OJE
Type: protein
Length: 1,194 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dr alpha chain precursor; HLA class II…
UniProt: P01903, P04229, Q48898
Ligands: PO4
Pockets: 14 · best druggability 0.62

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	HLA class II histocompatibility antigen, dr alpha chain precursor	protein	180	14% helix, 46% strand	P01903
B, F	HLA class II histocompatibility antigen, DRB1-1 beta chain precursor	protein	190	19% helix, 45% strand	P04229
C, G	Haemagglutinin peptide 306-318	protein	13	0% helix, 8% strand	—
D, H	Superantigen	protein	214	66% helix, 0% strand	Q48898

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains A, C, D, E, G, H

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	314	0.62	0.79	42	PO4
2	275	0.60	0.80	36	empty
3	245	0.58	0.79	32	PO4
4	180	0.53	0.78	23	empty
5	206	0.52	0.77	31	empty

Interfaces

13 interfaces between chains.

A–B · 2586 Å² buried · 42 hydrogen bonds · protein-protein
E–F · 2553 Å² buried · 44 hydrogen bonds · protein-protein
D–H · 892 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 773 Å² buried · 15 hydrogen bonds · protein-protein
E–H · 753 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 6 modified (disulfide, engineered).

Compared structures

2OJE · Mycoplasma arthritidis-derived mitogen complexed with class II MHC molecule HLA-DR1/HA… · the same entry in another collection · chain H against H, TM-score 1.00
P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P01903
Every structure of UniProt P04229
Every structure of UniProt Q48898
Elsewhere: RCSB PDB 2OJE · PDBe 2OJE · UniProt P01903 · UniProt P04229 · UniProt Q48898

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