MolNFT v1 · #38305 · protein
Human class I MHC HLA-A2 in complex with the decameric melan-A/MART- 1(26-35) peptide
2GT9 · HLA class I histocompatibility antigen: “Human class I MHC HLA-A2 in complex with the decameric melan-A/MART- 1(26-35) peptide”. X-ray diffraction, 1 ligand (NA), 9 pockets (best druggability 0.78). MolNFT v1 #38305 on GenesisL1: 3D…
- PDB
- 2GT9
- 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; Beta-2-microglobulin; Melan-A/MART-1(26-35)…
- UniProt
- Q9TQH5, P61769, Q16655
- Ligands
- NA
- Pockets
- 9 · 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 | protein | 275 | 28% helix, 40% strand | Q9TQH5 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Melan-A/MART-1(26-35) peptide | protein | 10 | 0% helix, 0% strand | Q16655 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, E
- 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.78 | 0.80 | 82 | GOL |
| 2 | 779 | 0.72 | 0.78 | 74 | GOL |
| 3 | 153 | 0.53 | 0.80 | 29 | empty |
| 4 | 124 | 0.51 | 0.80 | 23 | GOL |
| 5 | 147 | 0.48 | 0.78 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1442 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1432 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 829 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 827 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 624 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2GT9 · Human Class I MHC HLA-A2 in complex with the decameric Melan-A/MART-1(26-35) peptide · 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
- Q16655 · AlphaFold monomer V2.0 prediction for melanoma antigen recognized by T-cells 1 (Q16655) · a predicted model of the same protein · chain C against A, TM-score 0.25
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 Q9TQH5
- Every structure of UniProt P61769
- Every structure of UniProt Q16655
- Elsewhere: RCSB PDB 2GT9 · PDBe 2GT9 · UniProt Q9TQH5 · UniProt P61769 · UniProt Q16655
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