Research workbench
Structure of the H2DB-TCR ternary complex with HSF2 melanoma neoantigen
Analyse Structure of the H2DB-TCR ternary complex with HSF2 melanoma neoantigen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NA5
- Type
- protein
- Length
- 804 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; Heat shock…
- UniProt
- P01899, P61769, P38533
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 278 | 27% helix, 40% strand | P01899 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Heat shock factor protein 2 | protein | 9 | 0% helix, 0% strand | P38533 |
| D | 47BE7 TCR alpha chain | protein | 180 | 7% helix, 51% strand | — |
| E | 47BE7 TCR beta chain | protein | 238 | 6% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, E
- GOL · Glycerol · additive · 13 copies · chains A, B, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.70 | 0.76 | 71 | GOL, SO4 |
| 2 | 879 | 0.69 | 0.75 | 68 | GOL |
| 3 | 322 | 0.59 | 0.77 | 40 | GOL |
| 4 | 61 | 0.52 | 0.87 | 13 | empty |
| 5 | 67 | 0.42 | 0.81 | 16 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2074 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1305 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 420 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 249 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7NA5 · Structure of the H2DB-TCR ternary complex with HSF2 melanoma neoantigen · the same entry in another collection · chain B against B, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P38533 · AlphaFold monomer V2.0 prediction for heat shock factor protein 2 (P38533) · a predicted model of the same protein · chain C against A, TM-score 0.43
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 P01899
- Every structure of UniProt P61769
- Every structure of UniProt P38533
- Elsewhere: RCSB PDB 7NA5 · PDBe 7NA5 · UniProt P01899 · UniProt P61769 · UniProt P38533
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