Research workbench
TCR55 in complex with PEP20/HLA-B35
Analyse TCR55 in complex with PEP20/HLA-B35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BJ8
- Type
- protein
- Length
- 822 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-35 alpha chain; Beta-2-microglobulin; TCR 55…
- UniProt
- P30685, P61769, Q6IRV4, K7N5M4
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-35 alpha chain | protein | 274 | 28% helix, 39% strand | P30685 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P61769 |
| D | TCR 55 alpha chain | protein | 201 | 5% helix, 45% strand | Q6IRV4 |
| H | TCR 55 beta chain | protein | 242 | 8% helix, 49% strand | K7N5M4 |
| C | Val-pro-leu-thr-glu-asp-ala-glu-leu | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, D, H
- GOL · Glycerol · additive · 27 copies · chains A, B, C, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.77 | 0.97 | 23 | GOL |
| 2 | 1000 | 0.76 | 0.78 | 78 | GOL |
| 3 | 445 | 0.68 | 0.80 | 38 | GOL |
| 4 | 334 | 0.54 | 0.74 | 38 | GOL |
| 5 | 118 | 0.48 | 0.79 | 22 | empty |
Interfaces
7 interfaces between chains.
- D–H · 2362 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1163 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 844 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 532 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 388 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 P30685
- Every structure of UniProt P61769
- Every structure of UniProt Q6IRV4
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 6BJ8 · PDBe 6BJ8 · UniProt P30685 · UniProt P61769 · UniProt Q6IRV4 · UniProt K7N5M4
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