MolNFT v1 · #38328 · protein
Human class I MHC HLA-A2 in complex with the nonameric melan-A/MART- 1(27-35) peptide having A27L substitution
2GTW · HLA-A*0201 heavy chain: “Human class I MHC HLA-A2 in complex with the nonameric melan-A/MART- 1(27-35) peptide having A27L substitution”. X-ray diffraction, 1 ligand (NA), 9 pockets (best druggability 0.78). MolNFT v1 #38328 on…
- PDB
- 2GTW
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-A*0201 heavy chain; Beta-2-microglobulin; Octapeptide from melan-A/MART-1
- 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-A*0201 heavy chain | protein | 275 | 28% helix, 39% strand | Q9TQH5 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Octapeptide from melan-A/MART-1 | protein | 9 | 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
- FMT · Formic acid · additive · 4 copies · chains A, B, C, D, F
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 | 1029 | 0.78 | 0.80 | 92 | GOL |
| 2 | 688 | 0.70 | 0.78 | 69 | GOL |
| 3 | 162 | 0.53 | 0.80 | 31 | empty |
| 4 | 151 | 0.53 | 0.80 | 30 | FMT |
| 5 | 148 | 0.49 | 0.78 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1441 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1419 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 762 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 748 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 676 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2GTW · Human Class I MHC HLA-A2 in complex with the nonameric Melan-A/MART-1(27-35) 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 0.99
- 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 0.36
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 2GTW · PDBe 2GTW · UniProt Q9TQH5 · UniProt P61769 · UniProt Q16655
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