MolNFT v1 · #156942 · protein
Crystal structure of the MCD1D/XXP (JJ295) /inktcr ternary complex
6MJQ · T cell receptor alpha variable 11,T cell receptor alpha…: “Crystal structure of the MCD1D/XXP (JJ295) /inktcr ternary complex”. X-ray diffraction, 6 ligands (JUD, NAG, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #156942 on…
- PDB
- 6MJQ
- Type
- protein
- Length
- 1,623 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
- JUD, NAG, BMA, FUC, MAN, NA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 8% 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 | 1% helix, 47% strand | A0A0B4J1J9, K7N5M3 |
| D | Beta-CHAIN,T cell receptor CHAIN,T cell receptor beta constant 2, chimeric protein | protein | 240 | 6% helix, 48% strand | A2NTY6, A0N8J3, A0A5B9 |
| A, E | Antigen-presenting glycoprotein CD1D1 | protein | 274 | 24% helix, 41% strand | A0A0R4J090 |
| B, F | Beta-2-microglobulin | protein | 97 | 0% helix, 48% strand | P01887 |
| 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 | 201 | 1% helix, 47% strand | A0A0B4J1J9, K7N5M3 |
| H | Beta-CHAIN,T cell receptor CHAIN,T cell receptor beta constant 2, chimeric protein | protein | 239 | 6% helix, 48% strand | A2NTY6, A0N8J3, A0A5B9 |
Ligands and binding sites
- JUD · N-{(2S,3S,4R)-3,4-dihydroxy-1-[(4-O-{[4-(trifluoromethyl)phenyl]methyl}-alpha-D-galactopyranosyl)oxy]octadecan-2-yl}hexacosanamide · ligand · 2 copies · chains C, A, E, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, E
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, E
- MAN · alpha-D-mannopyranose · sugar
- NA · Sodium ion · metal · 3 copies · chains D, H
- GOL · Glycerol · additive · 3 copies · chains C, D, E, 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 | 901 | 0.86 | 0.88 | 78 | JUD |
| 2 | 889 | 0.86 | 0.87 | 74 | JUD |
| 3 | 1044 | 0.72 | 0.76 | 84 | empty |
| 4 | 1011 | 0.71 | 0.75 | 74 | empty |
| 5 | 401 | 0.65 | 0.79 | 51 | GOL |
Interfaces
11 interfaces between chains.
- C–D · 2117 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 2108 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1204 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1196 Ų buried · 11 hydrogen bonds · protein-protein
- E–G · 482 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6MJQ · Crystal structure of the mCD1d/xxp (JJ295) /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 6MJQ · PDBe 6MJQ · UniProt A0A0B4J1J9 · UniProt K7N5M3 · UniProt A2NTY6 · UniProt A0N8J3 · UniProt A0A5B9 · UniProt A0A0R4J090 · UniProt P01887
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