MolNFT v1 · #143018 · protein
Human class I MHC HLA-A2 in complex with synthetic peptide mmwdrglgmm
6AMT · HLA class I histocompatibility antigen, a-2 alpha chain: “Human class I MHC HLA-A2 in complex with synthetic peptide mmwdrglgmm”. X-ray diffraction, 9 pockets (best druggability 0.77). MolNFT v1 #143018 on GenesisL1: 3D structure…
- PDB
- 6AMT
- Type
- protein
- Length
- 766 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
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 274 | 26% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Met-met-TRP-asp-arg-gly-leu-gly-met-met | protein | 10 | 0% helix, 0% strand | — |
| E | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P61769 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.77 | 0.79 | 90 | empty |
| 2 | 757 | 0.70 | 0.77 | 73 | empty |
| 3 | 187 | 0.51 | 0.77 | 34 | empty |
| 4 | 150 | 0.48 | 0.78 | 23 | empty |
| 5 | 174 | 0.48 | 0.76 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1348 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1248 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 934 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 920 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 672 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6AMT · Human Class I MHC HLA-A2 in complex with synthetic peptide MMWDRGLGMM · 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 6AMT · PDBe 6AMT · UniProt P01892 · UniProt P61769
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