Research workbench
Mouse TCR I.29 in complex with IAG7-P8E9E6SS
Analyse Mouse TCR I.29 in complex with IAG7-P8E9E6SS in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DFS
- Type
- protein
- Length
- 779 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mouse TCR alpha chain; Mouse TCR beta chain; H-2 class II histocompatibility antigen, a-D…
- UniProt
- P04228, Q31135
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mouse TCR alpha chain | protein | 207 | 1% helix, 43% strand | — |
| B | Mouse TCR beta chain | protein | 241 | 6% helix, 49% strand | — |
| C | H-2 class II histocompatibility antigen, a-D alpha chain | protein | 181 | 12% helix, 39% strand | P04228 |
| D | H2-AB1 protein | protein | 150 | 19% helix, 33% strand | Q31135 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.72 | 0.76 | 93 | empty |
| 2 | 266 | 0.59 | 0.79 | 46 | empty |
| 3 | 203 | 0.55 | 0.79 | 31 | empty |
| 4 | 170 | 0.47 | 0.76 | 30 | empty |
| 5 | 136 | 0.43 | 0.76 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3042 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2185 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 509 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 315 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 124 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
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 P04228
- Every structure of UniProt Q31135
- Elsewhere: RCSB PDB 6DFS · PDBe 6DFS · UniProt P04228 · UniProt Q31135
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