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Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity through interactions with nk-cell receptors

Analyse Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IUE
Type: protein
Length: 1,525 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cdna FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility…
UniProt: B3KUD8, P61769
Ligands: NAG
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 8 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Cdna FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F	protein	275	26% helix, 41% strand	B3KUD8
B	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
F	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
G	Cdna FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F	protein	274	28% helix, 40% strand	B3KUD8
H, J	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
I	Cdna FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F	protein	275	27% helix, 40% strand	B3KUD8
K, L, M	Peptide leu-ile-leu-arg-TRP-glu-gln-asp	protein	7	0% helix, 0% strand	—
N	Peptide leu-ile-leu-arg-TRP-glu-gln-asp	protein	8	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains I

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	625	0.70	0.78	53	empty
2	646	0.70	0.78	58	empty
3	548	0.68	0.78	49	empty
4	509	0.67	0.78	40	empty
5	246	0.54	0.77	33	empty

Interfaces

13 interfaces between chains.

A–B · 1310 Å² buried · 14 hydrogen bonds · protein-protein
I–J · 1289 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1273 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1236 Å² buried · 16 hydrogen bonds · protein-protein
A–K · 830 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5IUE · Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity through… · the same entry in another collection · chain N against N, TM-score 1.00

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 B3KUD8
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5IUE · PDBe 5IUE · UniProt B3KUD8 · UniProt P61769

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