Research workbench
Structure of 5F3 TCR in complex with HLA-A2/MART-1
Analyse Structure of 5F3 TCR in complex with HLA-A2/MART-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D7G
- Type
- protein
- Length
- 792 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MART1 peptide-beta-2-microglobulin-HLA-A*02 chimera; Tra@ protein; T-cell receptor gamma…
- UniProt
- P61769, P01892, Q6PJ56
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MART1 peptide-beta-2-microglobulin-HLA-A*02 chimera | protein | 386 | 20% helix, 41% strand | P61769, P01892 |
| D | Tra@ protein | protein | 198 | 5% helix, 52% strand | Q6PJ56 |
| E | T-cell receptor gamma variable 8,T-cell receptor gamma-2 chain C region | protein | 208 | 5% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains 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 | 673 | 0.71 | 0.78 | 75 | empty |
| 2 | 353 | 0.63 | 0.78 | 59 | empty |
| 3 | 339 | 0.60 | 0.77 | 44 | empty |
| 4 | 81 | 0.57 | 0.87 | 22 | empty |
| 5 | 110 | 0.44 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- D–E · 1826 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 628 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
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 P61769
- Every structure of UniProt P01892
- Every structure of UniProt Q6PJ56
- Elsewhere: RCSB PDB 6D7G · PDBe 6D7G · UniProt P61769 · UniProt P01892 · UniProt Q6PJ56
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