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An alpha-beta T cell receptor (TCR) heterodimer in complex with an anti-TCR Fab fragment derived from a mitogenic antibody
Analyse An alpha-beta T cell receptor (TCR) heterodimer in complex with an anti-TCR Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NFD
- Type
- protein
- Length
- 1,752 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N15 alpha-beta T-cell receptor; H57 Fab
- UniProt
- P01852
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | N15 alpha-beta T-cell receptor | protein | 203 | 5% helix, 43% strand | — |
| B, D | N15 alpha-beta T-cell receptor | protein | 239 | 8% helix, 48% strand | P01852 |
| E, G | H57 Fab | protein | 212 | 8% helix, 44% strand | — |
| F, H | H57 Fab | protein | 222 | 5% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, F, C, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.75 | 0.77 | 75 | empty |
| 2 | 1093 | 0.72 | 0.76 | 87 | empty |
| 3 | 488 | 0.69 | 0.80 | 56 | empty |
| 4 | 568 | 0.64 | 0.75 | 60 | empty |
| 5 | 318 | 0.61 | 0.79 | 41 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2286 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2240 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1874 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1793 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 539 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 1NFD · An alpha-beta T cell receptor (TCR) heterodimer in complex with an anti-TCR Fab fragment… · the same entry in another collection · chain H against H, TM-score 1.00
- P01852 · AlphaFold monomer V2.0 prediction for T-cell receptor beta-1 chain C region (P01852) · a predicted model of the same protein · chain B against A, TM-score 0.52
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 P01852
- Elsewhere: RCSB PDB 1NFD · PDBe 1NFD · UniProt P01852
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