MolNFT v2 · #157979 · protein
Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex
6MJI: “Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex”. X-ray diffraction at 2.3, 6 ligands (JTD, NAG, BMA). MolNFT v2 #157979 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MJI
- Type
- protein
- Length
- 809 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens; Mus musculus
- UniProt
- A0A0B4J1J9, K7N5M3, A2NTY6, A0N8J3, A0A5B9, A0A0R4J090, P01887
- Ligands
- JTD, NAG, BMA, MAN, FUC, NA
Structure
x-ray diffraction · resolution 2.3 · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | — | protein | 203 | — | A0A0B4J1J9, K7N5M3 |
| D | — | protein | 239 | — | A2NTY6, A0N8J3, A0A5B9 |
| A | — | protein | 270 | — | A0A0R4J090 |
| B | — | protein | 97 | — | 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.
Compared structures
- 6MJI · Crystal structure of the MCD1D/XXS (JJ304) /inktcr ternary complex · the same entry in another collection · chain A against A, 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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