Research workbench
The complex between TCR A7B2 and human class I MHC HLA-A0201-WT1 with the bound rmfpnapyl peptide.
Analyse The complex between TCR A7B2 and human class I MHC HLA-A0201-WT1 with the bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RSY
- Type
- protein
- Length
- 1,634 residues
- Chains
- 10
- 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
- 20 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 25% helix, 39% strand | P01892 |
| B, G | Beta-2-microglobulin | protein | 100 | 0% helix, 48% strand | P61769 |
| C, H | Arg-met-phe-pro-asn-ala-pro-tyr-leu | protein | 9 | 0% helix, 0% strand | — |
| D | A7B2 alpha chain | protein | 192 | 2% helix, 39% strand | — |
| E, J | DMF4 beta chain | protein | 242 | 7% helix, 49% strand | — |
| F | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 274 | 24% helix, 37% strand | P01892 |
| I | A7B2 alpha chain | protein | 191 | 3% helix, 38% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.75 | 0.79 | 77 | empty |
| 2 | 969 | 0.74 | 0.77 | 68 | empty |
| 3 | 871 | 0.74 | 0.78 | 106 | empty |
| 4 | 522 | 0.70 | 0.80 | 58 | EDO |
| 5 | 655 | 0.69 | 0.78 | 60 | EDO |
Interfaces
18 interfaces between chains.
- D–E · 2316 Ų buried · 29 hydrogen bonds · protein-protein
- I–J · 2307 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1453 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1352 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 957 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6RSY · The complex between TCR a7b2 and human Class I MHC HLA-A0201-WT1 with the bound RMFPNAPYL… · the same entry in another collection · chain J against J, 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 0.98
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 6RSY · PDBe 6RSY · UniProt P01892 · UniProt P61769
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