Research workbench
Noncanonical binding of single-chain A6 TCR variant S3-4 in complex with TAX/HLA-A2
Analyse Noncanonical binding of single-chain A6 TCR variant S3-4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UZ1
- Type
- protein
- Length
- 1,212 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- A0A5B8RNS7, P61769
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | MHC class I antigen, a-2 alpha chain | protein | 275 | 23% helix, 41% strand | A0A5B8RNS7 |
| B, G | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, H | Leu-leu-phe-gly-tyr-pro-val-tyr-val | protein | 9 | 0% helix, 0% strand | — |
| I | T cell receptor, alpha chain | protein | 110 | 3% helix, 52% strand | — |
| J | T cell receptor, beta chain | protein | 114 | 3% helix, 46% strand | — |
| D | T cell receptor, alpha chain | protein | 108 | 3% helix, 51% strand | — |
| E | T cell receptor, beta chain | protein | 112 | 3% helix, 46% strand | — |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.81 | 0.87 | 59 | MES |
| 2 | 840 | 0.80 | 0.83 | 80 | MES |
| 3 | 115 | 0.50 | 0.81 | 23 | empty |
| 4 | 91 | 0.49 | 0.83 | 21 | empty |
| 5 | 83 | 0.49 | 0.83 | 16 | empty |
Interfaces
18 interfaces between chains.
- F–G · 1419 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1358 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 882 Ų buried · 13 hydrogen bonds · protein-protein
- F–H · 872 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 772 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6UZ1 · Noncanonical binding of single-chain A6 TCR variant S3-4 in complex with Tax/HLA-A2 · the same entry in another collection · chain E against E, TM-score 1.00
- 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 A0A5B8RNS7
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6UZ1 · PDBe 6UZ1 · UniProt A0A5B8RNS7 · UniProt P61769
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