MolNFT v1 · #94726 · protein

Structure of human MHC class II protein HLA-DR1 carrying an influenza hemagglutinin peptide partially filling the binding groove

4I5B · HLA class II histocompatibility antigen, dr alpha chain: “Structure of human MHC class II protein HLA-DR1 carrying an influenza hemagglutinin peptide partially filling…”. X-ray diffraction, 11 pockets (best druggability 0.69).…

PDB: 4I5B
Type: protein
Length: 772 residues
Chains: 6
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
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 6 distinct chains · 16% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dr alpha chain	protein	180	15% helix, 44% strand	P01903
B	HLA class II histocompatibility antigen, DRB1-1 beta chain	protein	192	19% helix, 45% strand	P04229
C	Truncated hemagglutinin peptide	protein	12	0% helix, 0% strand	—
D	HLA class II histocompatibility antigen, dr alpha chain	protein	187	13% helix, 44% strand	P01903
E	HLA class II histocompatibility antigen, DRB1-1 beta chain	protein	190	18% helix, 45% strand	P04229
F	Truncated hemagglutinin peptide	protein	11	0% helix, 0% strand	—

Pockets

11 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	328	0.69	0.83	40	empty
2	134	0.52	0.81	28	empty
3	69	0.46	0.83	22	empty
4	66	0.43	0.82	16	empty
5	64	0.42	0.82	12	empty

Interfaces

10 interfaces between chains.

D–E · 2579 Å² buried · 51 hydrogen bonds · protein-protein
A–B · 2564 Å² buried · 45 hydrogen bonds · protein-protein
B–C · 613 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 587 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 541 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4I5B · Structure of human MHC class II protein HLA-DR1 carrying an influenza hemagglutinin… · the same entry in another collection · chain F against F, 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
Elsewhere: RCSB PDB 4I5B · PDBe 4I5B · UniProt P01903 · UniProt P04229

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