MolNFT v1 · #114795 · protein
HLA-A02 carrying rqwgpdpaav
5C0F · HLA class I histocompatibility antigen, a-2 alpha chain: “HLA-A02 carrying rqwgpdpaav”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.68). MolNFT v1 #114795 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5C0F
- Type
- protein
- Length
- 387 residues
- Chains
- 3
- 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; Marker…
- UniProt
- P01892, P61769
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 277 | 26% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Marker peptide | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, C
- GOL · Glycerol · additive · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.68 | 0.77 | 54 | EDO |
| 2 | 91 | 0.42 | 0.79 | 22 | EDO |
| 3 | 60 | 0.42 | 0.82 | 18 | EDO |
| 4 | 51 | 0.35 | 0.79 | 15 | empty |
| 5 | 55 | 0.29 | 0.76 | 16 | SO4, EDO |
Interfaces
2 interfaces between chains.
- A–B · 1373 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 888 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 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 5C0F · PDBe 5C0F · UniProt P01892 · UniProt P61769
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