Research workbench
Structure of the HLA-E-VMAPRTLIL/KK50.4 TCR complex
Analyse Structure of the HLA-E-VMAPRTLIL/KK50.4 TCR complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ESV
- Type
- protein
- Length
- 816 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, alpha chain E; Beta-2-microglobulin; Vmaprtlil…
- UniProt
- P13747, P61769, P01848, P01850
- Ligands
- IOD
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, alpha chain E | protein | 268 | 26% helix, 38% strand | P13747 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| P | Vmaprtlil peptide from CMV GPUL40 | protein | 9 | 0% helix, 0% strand | — |
| D | KK50.4 T cell receptor alpha chain | protein | 199 | 3% helix, 41% strand | P01848 |
| E | KK50.4 T cell receptor beta chain | protein | 240 | 7% helix, 50% strand | P01850 |
Ligands and binding sites
- IOD · Iodide ion · ion · 5 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.70 | 0.79 | 50 | empty |
| 2 | 902 | 0.70 | 0.75 | 76 | IOD |
| 3 | 254 | 0.61 | 0.80 | 30 | empty |
| 4 | 111 | 0.46 | 0.79 | 23 | empty |
| 5 | 129 | 0.45 | 0.77 | 19 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2157 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1453 Ų buried · 19 hydrogen bonds · protein-protein
- A–P · 883 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 543 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 426 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2ESV · Structure of the HLA-E-VMAPRTLIL/KK50.4 TCR complex · the same entry in another collection · chain E against E, 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
- P13747 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P01850 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 1 (P01850) · a predicted model of the same protein · chain E against A, TM-score 0.53
- P01848 · AlphaFold monomer V2.0 prediction for T cell receptor alpha chain constant (P01848) · a predicted model of the same protein · chain D against A, TM-score 0.44
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 P13747
- Every structure of UniProt P61769
- Every structure of UniProt P01848
- Every structure of UniProt P01850
- Elsewhere: RCSB PDB 2ESV · PDBe 2ESV · UniProt P13747 · UniProt P61769 · UniProt P01848 · UniProt P01850
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