MolNFT v1 · #126829 · protein
Human leukocyte antigen A02 presenting ilakflhwl, in complex with cognate T-cell receptor
5MEN · HLA class I histocompatibility antigen, a-2 alpha chain: “Human leukocyte antigen A02 presenting ilakflhwl, in complex with cognate T-cell receptor”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 5MEN
- Type
- protein
- Length
- 825 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- P01892, P61769, A0A0B4J277, K7N5M3, A0A0K0K1A5, K7N5M4
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% helix, 39% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Ile-leu-ala-lys-phe-leu-his-TRP-leu | protein | 9 | 0% helix, 0% strand | — |
| D | Protein TRAV22,HUMAN nkt TCR alpha chain | protein | 200 | 2% helix, 47% strand | A0A0B4J277, K7N5M3 |
| E | Protein TRBV6-5,HUMAN nkt TCR beta chain | protein | 240 | 6% helix, 49% strand | A0A0K0K1A5, K7N5M4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, D, E
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.74 | 0.77 | 87 | empty |
| 2 | 698 | 0.69 | 0.77 | 54 | SO4, EDO |
| 3 | 134 | 0.46 | 0.77 | 24 | empty |
| 4 | 67 | 0.45 | 0.82 | 17 | EDO |
| 5 | 94 | 0.42 | 0.78 | 20 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2180 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1360 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 914 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 637 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 338 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5MEN · Human Leukocyte Antigen A02 presenting ILAKFLHWL, in complex with cognate T-Cell Receptor · 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 0.99
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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt A0A0B4J277
- Every structure of UniProt K7N5M3
- Every structure of UniProt A0A0K0K1A5
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 5MEN · PDBe 5MEN · UniProt P01892 · UniProt P61769 · UniProt A0A0B4J277 · UniProt K7N5M3 · UniProt A0A0K0K1A5 · UniProt K7N5M4
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