MolNFT v1 · #156926 · protein
Crystal structure of the MCD1D/XXO (JJ294) /inktcr ternary complex
6MJA · T cell receptor alpha variable 11,T cell receptor alpha…: “Crystal structure of the MCD1D/XXO (JJ294) /inktcr ternary complex”. X-ray diffraction, 5 ligands (JTJ, NAG, BMA), 8 pockets (best druggability 0.86). MolNFT v1 #156926 on…
- PDB
- 6MJA
- Type
- protein
- Length
- 807 residues
- Chains
- 4
- 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
- JTJ, NAG, BMA, FUC, NA
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% 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 | 269 | 26% helix, 41% strand | A0A0R4J090 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
Ligands and binding sites
- JTJ · N-[(2S,3S,4R)-3,4-dihydroxy-1-({4-O-[(4-methylphenyl) methyl]-alpha-D-galactopyranosyl}oxy)octadecan-2-yl]hexacosanamide · ligand · chains C, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains C, D, A
- GOL · Glycerol · additive · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.86 | 0.87 | 75 | JTJ |
| 2 | 1037 | 0.71 | 0.75 | 72 | empty |
| 3 | 451 | 0.66 | 0.78 | 55 | empty |
| 4 | 184 | 0.49 | 0.76 | 29 | empty |
| 5 | 151 | 0.44 | 0.76 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2158 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1240 Ų buried · 12 hydrogen bonds · protein-protein
- C–A · 487 Ų buried · 9 hydrogen bonds · protein-protein
- D–A · 348 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6MJA · Crystal structure of the mCD1d/xxo (JJ294) /iNKTCR ternary complex · the same entry in another collection · chain C against C, 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 D 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 6MJA · PDBe 6MJA · UniProt A0A0B4J1J9 · UniProt K7N5M3 · UniProt A2NTY6 · UniProt A0N8J3 · UniProt A0A5B9 · UniProt A0A0R4J090 · UniProt P01887
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.