Research workbench
Structure of the HLA-E-VMAPRTLIL/GF4 TCR complex
Analyse Structure of the HLA-E-VMAPRTLIL/GF4 TCR complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W1V
- Type
- protein
- Length
- 3,302 residues
- Chains
- 20
- 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K, P | HLA class I histocompatibility antigen, alpha chain E | protein | 272 | 23% helix, 37% strand | P13747 |
| B, G, L, Q | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, H, M, R | Vmaprtlil peptide from CMV GPUL40 | protein | 9 | 0% helix, 0% strand | — |
| D, S | GF4 T cell receptor alpha chain | protein | 201 | 3% helix, 44% strand | — |
| E, J, O, T | GF4 T cell receptor beta chain | protein | 243 | 4% helix, 46% strand | — |
| F | HLA class I histocompatibility antigen, alpha chain E | protein | 272 | 23% helix, 36% strand | P13747 |
| I, N | GF4 T cell receptor alpha chain | protein | 202 | 3% helix, 45% 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 | 822 | 0.81 | 0.84 | 76 | empty |
| 2 | 263 | 0.72 | 0.87 | 37 | empty |
| 3 | 706 | 0.70 | 0.77 | 83 | empty |
| 4 | 59 | 0.70 | 0.97 | 21 | empty |
| 5 | 620 | 0.70 | 0.78 | 58 | empty |
Interfaces
38 interfaces between chains.
- I–J · 2218 Ų buried · 24 hydrogen bonds · protein-protein
- N–O · 2197 Ų buried · 24 hydrogen bonds · protein-protein
- S–T · 2132 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 2123 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1513 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 5W1V · Structure of the HLA-E-VMAPRTLIL/GF4 TCR complex · the same entry in another collection · chain K against K, 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 P13747
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5W1V · PDBe 5W1V · UniProt P13747 · UniProt P61769
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