Research workbench
Crystal structure of an inkt TCR in complex with CD1D- lysophosphatidylcholine
Analyse Crystal structure of an inkt TCR in complex with CD1D- lysophosphatidylcholine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TZV
- Type
- protein
- Length
- 1,235 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Invariant natural killer T cell receptor chain a; Invariant natural killer T cell…
- UniProt
- P15813, P61769
- Ligands
- LSC, D12, NAG, FUC
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Invariant natural killer T cell receptor chain a | protein | 196 | 4% helix, 49% strand | — |
| B | Invariant natural killer T cell receptor chain B | protein | 236 | 6% helix, 49% strand | — |
| C | Antigen-presenting glycoprotein CD1D | protein | 263 | 26% helix, 37% strand | P15813 |
| D | Beta-2-microglobulin | protein | 95 | 0% helix, 46% strand | P61769 |
| G | Invariant natural killer T cell receptor chain a | protein | 201 | 3% helix, 45% strand | — |
| H | Invariant natural killer T cell receptor chain B | protein | 244 | 6% helix, 47% strand | — |
Ligands and binding sites
- LSC · (4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide · ligand · chains C, G
- D12 · Dodecane · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- FUC · alpha-L-fucopyranose · sugar · chains C, D
- HEX · Hexane · additive · chains C
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.87 | 0.88 | 94 | LSC, HEX, D12 |
| 2 | 609 | 0.74 | 0.81 | 83 | empty |
| 3 | 347 | 0.61 | 0.77 | 38 | empty |
| 4 | 248 | 0.59 | 0.79 | 33 | empty |
| 5 | 235 | 0.58 | 0.79 | 32 | empty |
Interfaces
8 interfaces between chains.
- G–H · 2121 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1941 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1101 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 634 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 511 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3TZV · Crystal structure of an iNKT TCR in complex with CD1d-lysophosphatidylcholine · the same entry in another collection · chain C against C, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P15813
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3TZV · PDBe 3TZV · UniProt P15813 · UniProt P61769
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