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Human pre-T cell receptor crystal structure
Analyse Human pre-T cell receptor crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OF6
- Type
- protein
- Length
- 1,032 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T cell receptor beta chain; Pre T-cell antigen receptor alpha
- UniProt
- Q6ISU1
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T cell receptor beta chain | protein | 240 | 7% helix, 48% strand | — |
| B | T cell receptor beta chain | protein | 242 | 7% helix, 43% strand | — |
| C | T cell receptor beta chain | protein | 243 | 6% helix, 46% strand | — |
| D | Pre T-cell antigen receptor alpha | protein | 100 | 5% helix, 47% strand | Q6ISU1 |
| E | Pre T-cell antigen receptor alpha | protein | 104 | 3% helix, 44% strand | Q6ISU1 |
| F | Pre T-cell antigen receptor alpha | protein | 103 | 3% helix, 47% strand | Q6ISU1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.73 | 0.80 | 92 | empty |
| 2 | 152 | 0.54 | 0.81 | 31 | empty |
| 3 | 232 | 0.50 | 0.75 | 40 | empty |
| 4 | 118 | 0.49 | 0.80 | 31 | empty |
| 5 | 53 | 0.48 | 0.86 | 19 | empty |
Interfaces
7 interfaces between chains.
- B–E · 950 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 942 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 908 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 694 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 678 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 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 Q6ISU1
- Elsewhere: RCSB PDB 3OF6 · PDBe 3OF6 · UniProt Q6ISU1
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