Research workbench
Human leukocyte antigen A02 presenting ilakflhel
Analyse Human leukocyte antigen A02 presenting ilakflhel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MER
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- 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
- Ligands
- CA, SO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% helix, 39% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Ile-leu-ala-lys-phe-leu-his-glu-leu | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 10 copies · chains B, A, C, D, E
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C, D, E, F
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, E, B, D
- GOL · Glycerol · additive · 3 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.77 | 0.81 | 80 | SO4 |
| 2 | 652 | 0.71 | 0.79 | 58 | SO4, EDO, MES |
| 3 | 724 | 0.69 | 0.77 | 64 | EDO, MES, SO4 |
| 4 | 162 | 0.59 | 0.83 | 20 | empty |
| 5 | 58 | 0.55 | 0.88 | 16 | GOL, EDO |
Interfaces
7 interfaces between chains.
- D–E · 1432 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1421 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 880 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 873 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 414 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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
- Elsewhere: RCSB PDB 5MER · PDBe 5MER · UniProt P01892 · UniProt P61769
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