MolNFT v1 · #138456 · protein
Crystal structure of the unliganded PG90 TCR
5WJO · PG90 TCR alpha chain: “Crystal structure of the unliganded PG90 TCR”. X-ray diffraction, 2 ligands (NA, CL), 7 pockets (best druggability 0.78). MolNFT v1 #138456 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WJO
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PG90 TCR alpha chain; PG90 TCR beta chain
- Ligands
- NA, CL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PG90 TCR alpha chain | protein | 189 | 5% helix, 43% strand | — |
| B | PG90 TCR beta chain | protein | 248 | 7% helix, 48% strand | — |
| C | PG90 TCR alpha chain | protein | 198 | 5% helix, 42% strand | — |
| D | PG90 TCR beta chain | protein | 237 | 7% helix, 50% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, D
- CL · Chloride ion · ion · 9 copies · chains B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.78 | 0.80 | 70 | NA, EDO |
| 2 | 1090 | 0.75 | 0.78 | 69 | CL |
| 3 | 73 | 0.39 | 0.78 | 16 | empty |
| 4 | 70 | 0.38 | 0.79 | 18 | empty |
| 5 | 61 | 0.34 | 0.77 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2232 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2179 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 204 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5WJO · Crystal structure of the unliganded PG90 TCR · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5WJO · PDBe 5WJO
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