Research workbench
Crystal structure of the 226 TCR in complex with mcc-P5E/I-ek
Analyse Crystal structure of the 226 TCR in complex with mcc-P5E/I-ek in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QIW
- Type
- protein
- Length
- 773 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class II histocompatibility antigen, E-K alpha chain; MHC class II H2-ia-beta chain…
- UniProt
- P04224, Q31163, P00039
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class II histocompatibility antigen, E-K alpha chain | protein | 179 | 15% helix, 49% strand | P04224 |
| B | MHC class II H2-ia-beta chain | protein | 165 | 20% helix, 42% strand | Q31163 |
| C | TCR 226 alpha chain | protein | 178 | 6% helix, 53% strand | — |
| D | TCR 226 beta chain | protein | 238 | 10% helix, 50% strand | — |
| E | Mcc-P5E peptide | protein | 13 | 0% helix, 15% strand | P00039 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.74 | 0.78 | 65 | empty |
| 2 | 132 | 0.41 | 0.75 | 21 | empty |
| 3 | 60 | 0.35 | 0.78 | 17 | empty |
| 4 | 80 | 0.35 | 0.75 | 19 | empty |
| 5 | 69 | 0.32 | 0.75 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2656 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2186 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 668 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 626 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 492 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3QIW · Crystal structure of the 226 TCR in complex with MCC-p5E/I-Ek · the same entry in another collection · chain B against B, TM-score 1.00
- P04224 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, E-K alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P00039 · AlphaFold monomer V2.0 prediction for cytochrome C (P00039) · a predicted model of the same protein · chain E against A, TM-score 0.31
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 P04224
- Every structure of UniProt Q31163
- Every structure of UniProt P00039
- Elsewhere: RCSB PDB 3QIW · PDBe 3QIW · UniProt P04224 · UniProt Q31163 · UniProt P00039
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