MolNFT v1 · #20142 · protein

Crystal structure of the mam-MHC complex

1R5I · HLA class II histocompatibility antigen, dr alpha chain: “Crystal structure of the mam-MHC complex”. X-ray diffraction, 1 ligand (PO4), 14 pockets (best druggability 0.64). MolNFT v1 #20142 on GenesisL1: 3D structure, binding sites…

PDB: 1R5I
Type: protein
Length: 1,196 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
UniProt: P01903, P04229, P11133, Q48898
Ligands: PO4
Pockets: 14 · best druggability 0.64

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	protein	181	14% helix, 45% strand	P01903
B, F	HLA class II histocompatibility antigen, DRB1-1 beta chain	protein	190	19% helix, 45% strand	P04229
C, G	Hemagglutinin peptide	protein	13	0% helix, 8% strand	P11133
D, H	Superantigen	protein	214	68% 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	354	0.64	0.79	41	PO4
2	307	0.62	0.80	41	empty
3	235	0.59	0.80	30	PO4
4	262	0.56	0.77	31	empty
5	136	0.54	0.81	18	empty

Interfaces

13 interfaces between chains.

A–B · 2608 Å² buried · 46 hydrogen bonds · protein-protein
E–F · 2576 Å² buried · 42 hydrogen bonds · protein-protein
D–H · 901 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 788 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 763 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1R5I · Crystal structure of the MAM-MHC complex · the same entry in another collection · chain C against C, 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 0.95

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 P01903
Every structure of UniProt P04229
Every structure of UniProt P11133
Every structure of UniProt Q48898
Elsewhere: RCSB PDB 1R5I · PDBe 1R5I · UniProt P01903 · UniProt P04229 · UniProt P11133 · UniProt Q48898

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