Research workbench
1D4 TCR recognition of H2-Ld a1a2 A5 Peptide Complexes
Analyse 1D4 TCR recognition of H2-Ld a1a2 A5 Peptide Complexes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L9L
- Type
- protein
- Length
- 1,242 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.399
- Source
- Homo sapiens
- Molecule
- H2-Ld a1a2; T Cell Receptor; Ser-pro-ser-tyr-ala-tyr-his-gln-phe
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.399 · 4 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | H2-Ld a1a2 | protein | 175 | 38% helix, 32% strand | — |
| C, G | T Cell Receptor | protein | 198 | 4% helix, 43% strand | — |
| D, H | T Cell Receptor | protein | 239 | 8% helix, 50% strand | — |
| B, F | Ser-pro-ser-tyr-ala-tyr-his-gln-phe | protein | 9 | 0% helix, 0% strand | — |
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.74 | 0.77 | 105 | empty |
| 2 | 553 | 0.70 | 0.79 | 80 | empty |
| 3 | 145 | 0.57 | 0.83 | 29 | empty |
| 4 | 112 | 0.55 | 0.83 | 28 | empty |
| 5 | 106 | 0.54 | 0.84 | 28 | empty |
Interfaces
15 interfaces between chains.
- G–H · 2108 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2087 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 908 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 900 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 398 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6L9L · 1D4 TCR recognition of H2-ld A1A2 A5 peptide complexes · 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 6L9L · PDBe 6L9L
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