Research workbench
Crystal structure of the MCD1D/XXM (JJ290) /inktcr ternary complex
Analyse Crystal structure of the MCD1D/XXM (JJ290) /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
- 6MJJ
- Type
- protein
- Length
- 810 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
- JU4, NAG, 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 | 201 | 5% helix, 48% strand | A0A0B4J1J9, K7N5M3 |
| D | Beta-CHAIN,TCELL receptor CHAIN,T cell receptor beta constant 2, chimeric protein | protein | 239 | 6% helix, 49% strand | A2NTY6, A0N8J3, A0A5B9 |
| A | Antigen-presenting glycoprotein CD1D1 | protein | 273 | 26% helix, 42% strand | A0A0R4J090 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 48% strand | P01887 |
Ligands and binding sites
- JU4 · N-[(2S,3S,4R)-1-({4-O-[(3,4-dichlorophenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide · ligand · chains C, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- NA · Sodium ion · metal · 9 copies · chains C, D, A
- GOL · Glycerol · additive · 10 copies · chains C, D, A, B
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 | 917 | 0.86 | 0.87 | 79 | JU4 |
| 2 | 953 | 0.70 | 0.75 | 71 | GOL |
| 3 | 370 | 0.62 | 0.77 | 47 | GOL |
| 4 | 198 | 0.50 | 0.76 | 33 | GOL |
| 5 | 130 | 0.45 | 0.77 | 29 | NA, GOL |
Interfaces
4 interfaces between chains.
- C–D · 2093 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1160 Ų buried · 13 hydrogen bonds · protein-protein
- C–A · 479 Ų buried · 9 hydrogen bonds · protein-protein
- D–A · 371 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6MJJ · Crystal structure of the mCD1d/xxm (JJ290) /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 6MJJ · PDBe 6MJJ · UniProt A0A0B4J1J9 · UniProt K7N5M3 · UniProt A2NTY6 · UniProt A0N8J3 · UniProt A0A5B9 · UniProt A0A0R4J090 · UniProt P01887
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