MolNFT v1 · #9472 · protein
Crystal structure of a human VGAMMA9/VDELTA2 T cell receptor
1HXM · Gamma-delta T-cell receptor: “Crystal structure of a human VGAMMA9/VDELTA2 T cell receptor”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.74). MolNFT v1 #9472 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1HXM
- Type
- protein
- Length
- 1,744 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-delta T-cell receptor
- UniProt
- P03986
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Gamma-delta T-cell receptor | protein | 206 | 6% helix, 52% strand | — |
| B, D, F, H | Gamma-delta T-cell receptor | protein | 230 | 7% helix, 47% strand | P03986 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.74 | 0.77 | 107 | empty |
| 2 | 835 | 0.73 | 0.78 | 85 | empty |
| 3 | 536 | 0.71 | 0.80 | 80 | empty |
| 4 | 446 | 0.70 | 0.81 | 51 | empty |
| 5 | 361 | 0.62 | 0.78 | 35 | empty |
Interfaces
9 interfaces between chains.
- G–H · 1893 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1892 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1889 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1876 Ų buried · 17 hydrogen bonds · protein-protein
- D–G · 628 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1HXM · Crystal Structure of a Human Vgamma9/Vdelta2 T Cell Receptor · the same entry in another collection · chain H against H, TM-score 1.00
- P03986 · AlphaFold monomer V2.0 prediction for T cell receptor gamma constant 2 (P03986) · a predicted model of the same protein · chain B against A, TM-score 0.45
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 P03986
- Elsewhere: RCSB PDB 1HXM · PDBe 1HXM · UniProt P03986
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