Research workbench
Crystal structure of PG90 TCR-CD1B-pg complex
Analyse Crystal structure of PG90 TCR-CD1B-pg complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WKI
- Type
- protein
- Length
- 810 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1B; Beta-2-microglobulin; T-cell receptor alpha variable…
- UniProt
- P29016, P61769, A0A087WT03, Q6P4G7
- Ligands
- CUY, D3D, NAG, FUC, NA, CL
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1B | protein | 267 | 25% helix, 43% strand | P29016 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 49% strand | P61769 |
| D | T-cell receptor alpha variable 26-1,TRA@ protein | protein | 198 | 2% helix, 43% strand | A0A087WT03, Q6P4G7 |
| E | PG90 TCR beta chain | protein | 248 | 7% helix, 48% strand | — |
Ligands and binding sites
- CUY · tetracosyl octadecanoate · ligand · chains A
- D3D · (19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate · ligand · chains A, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains D, E
- CL · Chloride ion · ion · chains E
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, D, E
- ACT · Acetate ion · additive · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.87 | 0.88 | 107 | CUY, D3D |
| 2 | 1149 | 0.74 | 0.77 | 72 | empty |
| 3 | 415 | 0.68 | 0.80 | 42 | EDO |
| 4 | 138 | 0.48 | 0.78 | 26 | EDO |
| 5 | 80 | 0.40 | 0.79 | 17 | empty |
Interfaces
4 interfaces between chains.
- D–E · 2227 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1209 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 430 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 419 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5WKI · Crystal structure of PG90 TCR-CD1b-PG 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
- Every structure of UniProt A0A087WT03
- Every structure of UniProt Q6P4G7
- Elsewhere: RCSB PDB 5WKI · PDBe 5WKI · UniProt P29016 · UniProt P61769 · UniProt A0A087WT03 · UniProt Q6P4G7
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