Research workbench
868 TCR in complex with HLA A02 presenting slyntvatl
Analyse 868 TCR in complex with HLA A02 presenting slyntvatl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NME
- Type
- protein
- Length
- 1,654 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; Gag…
- UniProt
- P01892, P61769, O11793
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% helix, 39% strand | P01892 |
| B, G | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, H | Gag protein | protein | 9 | 0% helix, 0% strand | O11793 |
| D | T-cell receptor alpha chain | protein | 201 | 1% helix, 47% strand | — |
| E | Human T-cell receptor beta chain | protein | 242 | 7% helix, 51% strand | — |
| I | T-cell receptor alpha chain | protein | 200 | 2% helix, 48% strand | — |
| J | Human T-cell receptor beta chain | protein | 241 | 7% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, E, J
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, D, E, I, J
- GOL · Glycerol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.74 | 0.77 | 77 | empty |
| 2 | 1071 | 0.74 | 0.77 | 84 | empty |
| 3 | 614 | 0.67 | 0.77 | 59 | empty |
| 4 | 544 | 0.64 | 0.76 | 53 | empty |
| 5 | 317 | 0.56 | 0.76 | 39 | empty |
Interfaces
15 interfaces between chains.
- I–J · 2210 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 2092 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1377 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1340 Ų buried · 19 hydrogen bonds · protein-protein
- F–H · 830 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt O11793
- Elsewhere: RCSB PDB 5NME · PDBe 5NME · UniProt P01892 · UniProt P61769 · UniProt O11793
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