Research workbench
Crystal structure of the MCD1D/XXA (JJ239)/INKTCR ternary complex
Analyse Crystal structure of the MCD1D/XXA (JJ239)/INKTCR ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MIY
- Type
- protein
- Length
- 1,619 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha…
- UniProt
- A0A0B4J1J9, K7N5M3, A2NTY6, A0N8J3, A0A5B9, A0A0R4J090, P01887
- Ligands
- JTV, NAG, FUC, NA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,HUMAN nkt TCR alpha chain, chimeric protein | protein | 200 | 5% helix, 47% strand | A0A0B4J1J9, K7N5M3 |
| D | Beta-CHAIN,T cell receptor CHAIN,T cell receptor beta constant 2, chimeric protein | protein | 240 | 6% helix, 49% strand | A2NTY6, A0N8J3, A0A5B9 |
| A | Antigen-presenting glycoprotein CD1D1 | protein | 271 | 25% helix, 41% strand | A0A0R4J090 |
| B, F | Beta-2-microglobulin | protein | 98 | 0% helix, 48% strand | P01887 |
| E | Antigen-presenting glycoprotein CD1D1 | protein | 274 | 26% helix, 41% strand | A0A0R4J090 |
| G | T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,HUMAN nkt TCR alpha chain, chimeric protein | protein | 199 | 2% helix, 46% strand | A0A0B4J1J9, K7N5M3 |
| H | Beta-CHAIN,T cell receptor CHAIN,T cell receptor beta constant 2, chimeric protein | protein | 239 | 6% helix, 49% strand | A2NTY6, A0N8J3, A0A5B9 |
Ligands and binding sites
- JTV · N-{(2S,3S,4R)-1-[(4-O-benzyl-alpha-D-galactopyranosyl) oxy]-3,4-dihydroxyoctadecan-2-yl}hexacosanamide · ligand · 2 copies · chains C, A, E, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, E
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, E
- NA · Sodium ion · metal · 4 copies · chains C, D, G, H
- CL · Chloride ion · ion · chains D
- GOL · Glycerol · additive · 4 copies · chains A, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.85 | 0.87 | 79 | JTV |
| 2 | 878 | 0.85 | 0.87 | 81 | JTV |
| 3 | 1081 | 0.71 | 0.75 | 77 | empty |
| 4 | 1000 | 0.70 | 0.75 | 68 | NA |
| 5 | 429 | 0.65 | 0.78 | 51 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2175 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2137 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1278 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1246 Ų buried · 14 hydrogen bonds · protein-protein
- C–A · 480 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6MIY · Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex · the same entry in another collection · chain F against F, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
- A0A5B9 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 2 (A0A5B9) · a predicted model of the same protein · chain H against A, TM-score 0.53
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 A0A0B4J1J9
- Every structure of UniProt K7N5M3
- Every structure of UniProt A2NTY6
- Every structure of UniProt A0N8J3
- Every structure of UniProt A0A5B9
- Every structure of UniProt A0A0R4J090
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 6MIY · PDBe 6MIY · UniProt A0A0B4J1J9 · UniProt K7N5M3 · UniProt A2NTY6 · UniProt A0N8J3 · UniProt A0A5B9 · UniProt A0A0R4J090 · UniProt P01887
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