Research workbench
SILV44 T cell receptor bound to HLA-A2 presenting GP100 peptide (itdqvpfsv)
Analyse SILV44 T cell receptor bound to HLA-A2 presenting GP100 peptide (itdqvpfsv) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VM7
- Type
- protein
- Length
- 822 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SILV44 T cell receptor alpha chain; SILV44 T cell receptor beta chain; MHC class I…
- UniProt
- A0A5B8RNS7, P61769, P40967
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | SILV44 T cell receptor alpha chain | protein | 197 | 3% helix, 44% strand | — |
| E | SILV44 T cell receptor beta chain | protein | 241 | 6% helix, 49% strand | — |
| A | MHC class I antigen, a-2 alpha chain | protein | 275 | 25% helix, 40% strand | A0A5B8RNS7 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C | Melanocyte protein pmel | protein | 9 | 0% helix, 0% strand | P40967 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.77 | 0.79 | 90 | empty |
| 2 | 748 | 0.70 | 0.77 | 70 | empty |
| 3 | 155 | 0.54 | 0.80 | 24 | GOL |
| 4 | 316 | 0.52 | 0.73 | 38 | empty |
| 5 | 143 | 0.46 | 0.77 | 29 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2283 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1395 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 839 Ų buried · 16 hydrogen bonds · protein-protein
- E–A · 435 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 198 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6VM7 · SILv44 T cell receptor bound to HLA-A2 presenting gp100 peptide (ITDQVPFSV) · 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
- P40967 · AlphaFold monomer V2.0 prediction for melanocyte protein pmel (P40967) · a predicted model of the same protein · chain C against A, TM-score 0.46
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
- Every structure of UniProt P40967
- Elsewhere: RCSB PDB 6VM7 · PDBe 6VM7 · UniProt A0A5B8RNS7 · UniProt P61769 · UniProt P40967
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