Research workbench
Crystal structure of the MCD1D/DB06-1/INKTCR ternary complex
Analyse Crystal structure of the MCD1D/DB06-1/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
- 4ZAK
- Type
- protein
- Length
- 807 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Protein…
- UniProt
- P11609, P01887, A0A0B4J1J9, A0N4Z0, K7N5M3, A0A075B5J4, A0A5B9
- Ligands
- 4LX, NAG
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 267 | 25% helix, 40% strand | P11609 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P01887 |
| C | Protein TRAV11,VA14JA18/VB8.2,HUMAN nkt TCR alpha chain | protein | 203 | 3% helix, 47% strand | A0A0B4J1J9, A0N4Z0, K7N5M3 |
| D | T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C REGION,PROTEIN TRBC2,T-cell receptor beta-2 chain C region | protein | 239 | 6% helix, 49% strand | A0A075B5J4, A0A5B9 |
Ligands and binding sites
- 4LX · N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanethioamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.86 | 0.88 | 73 | 4LX |
| 2 | 798 | 0.67 | 0.74 | 73 | empty |
| 3 | 361 | 0.64 | 0.79 | 42 | empty |
| 4 | 233 | 0.51 | 0.76 | 35 | empty |
| 5 | 112 | 0.40 | 0.76 | 22 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2109 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1192 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 485 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 346 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4ZAK · Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
- P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · 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 P11609
- Every structure of UniProt P01887
- Every structure of UniProt A0A0B4J1J9
- Every structure of UniProt A0N4Z0
- Every structure of UniProt K7N5M3
- Every structure of UniProt A0A075B5J4
- Every structure of UniProt A0A5B9
- Elsewhere: RCSB PDB 4ZAK · PDBe 4ZAK · UniProt P11609 · UniProt P01887 · UniProt A0A0B4J1J9 · UniProt A0N4Z0 · UniProt K7N5M3 · UniProt A0A075B5J4 · UniProt A0A5B9
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