MolNFT v1 · #75651 · protein
Human class I MHC HLA-A2 in complex with the hud (G2L) peptide variant
3PWN · HLA class I histocompatibility antigen, a-2 alpha chain: “Human class I MHC HLA-A2 in complex with the hud (G2L) peptide variant”. X-ray diffraction, 8 pockets (best druggability 0.78). MolNFT v1 #75651 on GenesisL1: 3D structure…
- PDB
- 3PWN
- Type
- protein
- Length
- 768 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; Hud (G2L)…
- UniProt
- P01892, P61769
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 28% helix, 39% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Hud (G2L) peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.78 | 0.80 | 92 | GOL |
| 2 | 773 | 0.73 | 0.79 | 72 | GOL |
| 3 | 140 | 0.53 | 0.81 | 25 | GOL |
| 4 | 143 | 0.52 | 0.80 | 29 | GOL |
| 5 | 118 | 0.46 | 0.79 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1404 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1392 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 894 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 890 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 610 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3PWN · Human Class I MHC HLA-A2 in complex with the HuD (G2L) peptide variant · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 3PWN · PDBe 3PWN · UniProt P01892 · UniProt P61769
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