MolNFT v2 · #145129 · protein
Crystal structure of TCR-MHC-like molecule
6BNL · Antigen-presenting glycoprotein CD1d1: “Crystal structure of TCR-MHC-like molecule”. X-ray diffraction at 2.6, 2 ligands (QWV, NAG), 16 pockets (best druggability 0.86). MolNFT v2 #145129 on GenesisL1: 3D structure, binding sites…
- PDB
- 6BNL
- Type
- protein
- Length
- 1,589 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens; Mus musculus
- Molecule
- Antigen-presenting glycoprotein CD1d1; Beta-2-microglobulin; NKT Valpha14 (MOUSE) - 2C12…
- UniProt
- A0A0R4J090, P01887
- Ligands
- QWV, NAG
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.6 · 7 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1d1 | protein | 255 | 27% helix, 39% strand | A0A0R4J090 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 49% strand | P01887 |
| C | NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains | protein | 202 | 4% helix, 49% strand | — |
| D, H | NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains | protein | 240 | 6% helix, 48% strand | — |
| E | Antigen-presenting glycoprotein CD1d1 | protein | 260 | 27% helix, 40% strand | A0A0R4J090 |
| F | Beta-2-microglobulin | protein | 93 | 0% helix, 43% strand | P01887 |
| G | NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains | protein | 203 | 5% helix, 49% strand | — |
Ligands and binding sites
- QWV · N-[(2S,3R)-3-hydroxy-1-{[6-O-(3-phenylpropanoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide · ligand · 2 copies · chains A, C, E, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.86 | 0.88 | 76 | QWV |
| 2 | 789 | 0.86 | 0.88 | 77 | QWV |
| 3 | 847 | 0.72 | 0.77 | 77 | empty |
| 4 | 819 | 0.68 | 0.75 | 69 | empty |
| 5 | 792 | 0.65 | 0.74 | 68 | empty |
Interfaces
11 interfaces between chains.
- C–D · 2124 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 2122 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1145 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1119 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 477 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 A0A0R4J090
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 6BNL · PDBe 6BNL · UniProt A0A0R4J090 · UniProt P01887
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