MolNFT v1 · #156934 · protein
Crystal structure of the MCD1D/XXS (JJ304) /inktcr ternary complex
6MJI · T cell receptor alpha variable 11,T cell receptor alpha…: “Crystal structure of the MCD1D/XXS (JJ304) /inktcr ternary complex”. X-ray diffraction, 6 ligands (JTD, NAG, BMA), 9 pockets (best druggability 0.86). MolNFT v1 #156934 on…
- PDB
- 6MJI
- Type
- protein
- Length
- 809 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 joining 18,HUMAN nkt TCR alpha…
- UniProt
- A0A0B4J1J9, K7N5M3, A2NTY6, A0N8J3, A0A5B9, A0A0R4J090, P01887
- Ligands
- JTD, NAG, BMA, MAN, FUC, NA
- Pockets
- 9 · 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 joining 18,HUMAN nkt TCR alpha chain, chimeric protein | protein | 203 | 5% helix, 47% strand | A0A0B4J1J9, K7N5M3 |
| D | Beta-CHAIN,TCELL receptor CHAIN,T cell receptor beta constant 2 | protein | 239 | 6% helix, 49% strand | A2NTY6, A0N8J3, A0A5B9 |
| A | Antigen-presenting glycoprotein CD1D1 | protein | 270 | 27% helix, 41% strand | A0A0R4J090 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P01887 |
Ligands and binding sites
- JTD · N-[(2S,3S,4R)-1-{[4-O-(cyclopropylmethyl)-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
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains C, D
- GOL · Glycerol · additive · 6 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.86 | 0.87 | 79 | JTD |
| 2 | 901 | 0.68 | 0.74 | 67 | empty |
| 3 | 459 | 0.65 | 0.78 | 51 | GOL |
| 4 | 197 | 0.48 | 0.75 | 30 | empty |
| 5 | 130 | 0.46 | 0.77 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2111 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1182 Ų buried · 10 hydrogen bonds · protein-protein
- C–A · 479 Ų buried · 8 hydrogen bonds · protein-protein
- D–A · 365 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6MJI · Crystal structure of the mCD1d/xxs (JJ304) /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 6MJI · PDBe 6MJI · UniProt A0A0B4J1J9 · UniProt K7N5M3 · UniProt A2NTY6 · UniProt A0N8J3 · UniProt A0A5B9 · UniProt A0A0R4J090 · UniProt P01887
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