Research workbench
Structure of human D462-E4 TCR
Analyse Structure of human D462-E4 TCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XQQ
- Type
- protein
- Length
- 879 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRAV12-2 alpha chain; TRBV29-1
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRAV12-2 alpha chain | protein | 197 | 3% helix, 45% strand | — |
| B, D | TRBV29-1 | protein | 246 | 7% helix, 50% strand | — |
| C | TRAV12-2 alpha chain | protein | 190 | 2% helix, 48% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.81 | 0.89 | 50 | empty |
| 2 | 872 | 0.75 | 0.79 | 72 | empty |
| 3 | 649 | 0.69 | 0.78 | 72 | empty |
| 4 | 251 | 0.53 | 0.76 | 34 | empty |
| 5 | 119 | 0.47 | 0.79 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2026 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1892 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1075 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6XQQ · Structure of human D462-E4 TCR · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6XQQ · PDBe 6XQQ
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