Research workbench
Crystal structure of ELS4 TCR bound to HLA-B*3501 presenting EBV peptide eplpqgqltay at 1.7A
Analyse Crystal structure of ELS4 TCR bound to HLA-B*3501 presenting EBV peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NX5
- Type
- protein
- Length
- 3,268 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-B35; Beta-2-microglobulin; EBV peptide, eplpqgqltay; ELS4 TCR alpha chain; ELS4 TCR…
- UniProt
- O19626, P61769
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, K, Q | HLA-B35 | protein | 276 | 27% helix, 41% strand | O19626 |
| B, G, L, R | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, H, M, S | EBV peptide, eplpqgqltay | protein | 11 | 0% helix, 0% strand | — |
| D, I, N, T | ELS4 TCR alpha chain | protein | 188 | 2% helix, 50% strand | — |
| E, J, P, U | ELS4 TCR beta chain | protein | 243 | 7% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.80 | 0.81 | 123 | empty |
| 2 | 1135 | 0.79 | 0.81 | 113 | empty |
| 3 | 880 | 0.78 | 0.81 | 86 | empty |
| 4 | 927 | 0.76 | 0.79 | 77 | empty |
| 5 | 652 | 0.76 | 0.82 | 75 | empty |
Interfaces
48 interfaces between chains.
- I–J · 2212 Ų buried · 24 hydrogen bonds · protein-protein
- T–U · 2164 Ų buried · 25 hydrogen bonds · protein-protein
- N–P · 2157 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2055 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1439 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 2NX5 · Crystal structure of ELS4 TCR bound to HLA-B*3501 presenting EBV peptide EPLPQGQLTAY at… · the same entry in another collection · chain U against U, TM-score 1.00
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 O19626
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 2NX5 · PDBe 2NX5 · UniProt O19626 · UniProt P61769
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