Research workbench
Crystal structure of complex between D10 TCR and pmhc I-AK/CA
Analyse Crystal structure of complex between D10 TCR and pmhc I-AK/CA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D9K
- Type
- protein
- Length
- 1,218 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell receptor D10 (alpha chain); T-cell receptor D10 (beta chain); MHC I-ak a chain…
- UniProt
- P01910, P06343
- Ligands
- NAG, NDG
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | T-cell receptor D10 (alpha chain) | protein | 110 | 0% helix, 43% strand | — |
| B, F | T-cell receptor D10 (beta chain) | protein | 112 | 5% helix, 42% strand | — |
| C, G | MHC I-ak a chain (alpha chain) | protein | 183 | 14% helix, 44% strand | P01910 |
| D, H | MHC I-ak B chain (beta chain) | protein | 188 | 18% helix, 39% strand | P06343 |
| P, Q | Conalbumin peptide | protein | 16 | 0% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains C, D, G, H
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.69 | 0.79 | 74 | empty |
| 2 | 363 | 0.64 | 0.79 | 45 | empty |
| 3 | 184 | 0.56 | 0.80 | 20 | empty |
| 4 | 274 | 0.56 | 0.77 | 40 | empty |
| 5 | 245 | 0.55 | 0.77 | 34 | empty |
Interfaces
23 interfaces between chains.
- C–D · 2675 Ų buried · 50 hydrogen bonds · protein-protein
- G–H · 2663 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 859 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 830 Ų buried · 12 hydrogen bonds · protein-protein
- D–P · 793 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 1D9K · Crystal structure of complex between D10 TCR and pmhc I-AK/CA · the same entry in another collection · chain Q against Q, TM-score 1.00
- P01910 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-K alpha… · a predicted model of the same protein · chain C against A, TM-score 0.97
- P06343 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-K beta… · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P01910
- Every structure of UniProt P06343
- Elsewhere: RCSB PDB 1D9K · PDBe 1D9K · UniProt P01910 · UniProt P06343
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.