MolNFT v1 · #124724 · protein
Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity through interactions with nk-cell receptors
5KNM · Cdna FLJ39643 fis, clone SMINT2004023, highly similar to…: “Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity through interactions with nk-cell…”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best…
- PDB
- 5KNM
- Type
- protein
- Length
- 570 residues
- Chains
- 4
- 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, Q8NHL6
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cdna FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F | protein | 276 | 25% helix, 39% strand | B3KUD8 |
| B | Beta-2-microglobulin | protein | 101 | 0% helix, 49% strand | P61769 |
| D | Leukocyte immunoglobulin-like receptor subfamily B member 1 | protein | 187 | 4% helix, 30% strand | Q8NHL6 |
| N | Peptide ile-leu-arg-TRP-glu-gln | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.75 | 0.79 | 50 | empty |
| 2 | 186 | 0.74 | 0.90 | 24 | empty |
| 3 | 61 | 0.67 | 0.95 | 18 | empty |
| 4 | 466 | 0.67 | 0.79 | 48 | empty |
| 5 | 336 | 0.64 | 0.79 | 39 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1428 Ų buried · 15 hydrogen bonds · protein-protein
- A–N · 612 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 532 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 402 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5KNM · Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity through… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q8NHL6 · AlphaFold monomer V2.0 prediction for leukocyte immunoglobulin-like receptor subfamily B… · a predicted model of the same protein · chain D against A, TM-score 0.90
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
- Every structure of UniProt Q8NHL6
- Elsewhere: RCSB PDB 5KNM · PDBe 5KNM · UniProt B3KUD8 · UniProt P61769 · UniProt Q8NHL6
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