MolNFT v1 · #125219 · protein
Crystal structure of GEM42 TCR-CD1B-gmm complex
5L2K · T-cell surface glycoprotein CD1B: “Crystal structure of GEM42 TCR-CD1B-gmm complex”. X-ray diffraction, 7 ligands (6UL, 70E, NAG), 8 pockets (best druggability 0.90). MolNFT v1 #125219 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5L2K
- Type
- protein
- Length
- 801 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1B; Beta-2-microglobulin; GEM42 TCR alpha chain; GEM42 TCR…
- UniProt
- P29016, P61769
- Ligands
- 6UL, 70E, NAG, NA, CS, SO4, CL
- Pockets
- 8 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1B | protein | 276 | 24% helix, 42% strand | P29016 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| D | GEM42 TCR alpha chain | protein | 185 | 2% helix, 49% strand | — |
| E | GEM42 TCR beta chain | protein | 242 | 7% helix, 51% strand | — |
Ligands and binding sites
- 6UL · Tetracosyl palmitate · ligand · chains A
- 70E · 6-O-[(2R,3R)-3-hydroxy-2-tetradecyldocosanoyl]-alpha-L-idopyranose · ligand · chains A, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A, E
- CS · Cesium ion · metal · chains D
- SO4 · Sulfate ion · ion · 5 copies · chains A, E, D
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.90 | 0.92 | 80 | 6UL, 70E |
| 2 | 1107 | 0.72 | 0.76 | 81 | empty |
| 3 | 369 | 0.64 | 0.79 | 43 | empty |
| 4 | 206 | 0.56 | 0.79 | 35 | empty |
| 5 | 194 | 0.51 | 0.77 | 27 | SO4 |
Interfaces
4 interfaces between chains.
- D–E · 2160 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1342 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 447 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 386 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5L2K · Crystal structure of GEM42 TCR-CD1b-GMM complex · the same entry in another collection · chain A against A, TM-score 1.00
- P29016 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1B (P29016) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P29016
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5L2K · PDBe 5L2K · UniProt P29016 · UniProt P61769
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