Research workbench
Crystal structure of the public RA14 TCR in complex with the hcmv dominant NLV/HLA-A2 epitope
Analyse Crystal structure of the public RA14 TCR in complex with the hcmv dominant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GSN
- Type
- protein
- Length
- 825 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Hcmv PP65 fragment 495-503…
- UniProt
- P01892, P61769
- Ligands
- SO4, CL
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 274 | 23% helix, 34% strand | P01892 |
| P | Hcmv PP65 fragment 495-503 (nlvpmvatv) | protein | 9 | 0% helix, 0% strand | — |
| L | Beta-2-microglobulin | protein | 100 | 0% helix, 45% strand | P61769 |
| A | RA14 TCR alpha chain (TRAV24, TRAJ49) | protein | 199 | 2% helix, 36% strand | — |
| B | RA14 TCR beta chain (TRBV6-5, TRBD1, TRBJ1-2) | protein | 243 | 6% helix, 49% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.73 | 0.76 | 89 | empty |
| 2 | 706 | 0.70 | 0.77 | 62 | empty |
| 3 | 119 | 0.69 | 0.91 | 25 | empty |
| 4 | 155 | 0.56 | 0.81 | 22 | empty |
| 5 | 224 | 0.54 | 0.78 | 38 | CL |
Interfaces
7 interfaces between chains.
- A–B · 2207 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1408 Ų buried · 20 hydrogen bonds · protein-protein
- H–P · 773 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 436 Ų buried · 4 hydrogen bonds · protein-protein
- H–A · 416 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 3GSN · Crystal structure of the public RA14 TCR in complex with the HCMV dominant NLV/HLA-A2… · the same entry in another collection · chain B against B, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain L against A, TM-score 0.97
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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3GSN · PDBe 3GSN · UniProt P01892 · UniProt P61769
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