MolNFT v1 · #176851 · protein
Crystal structure of the cross-restricted T18A TCR and HLAB8101 bound to HIV-1 gag TL9 peptide
7DZM · MHC class I antigen: “Crystal structure of the cross-restricted T18A TCR and HLAB8101 bound to HIV-1 gag TL9 peptide”. X-ray diffraction, 9 pockets (best druggability 0.73). MolNFT v1 #176851 on GenesisL1: 3D structure, binding…
- PDB
- 7DZM
- Type
- protein
- Length
- 829 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Gag-pol polyprotein; Beta chain T18A TCR…
- UniProt
- I3ZN85, P61769, P03367
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 278 | 27% helix, 39% strand | I3ZN85 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C | Gag-pol polyprotein | protein | 9 | 0% helix, 0% strand | P03367 |
| D | Beta chain T18A TCR | protein | 241 | 7% helix, 52% strand | — |
| E | Alpha chain T18A TCR | protein | 201 | 5% helix, 42% strand | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.73 | 0.76 | 84 | empty |
| 2 | 502 | 0.69 | 0.79 | 52 | empty |
| 3 | 89 | 0.51 | 0.84 | 30 | empty |
| 4 | 63 | 0.46 | 0.83 | 18 | empty |
| 5 | 149 | 0.45 | 0.76 | 24 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2171 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1437 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 868 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 420 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 245 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7DZM · Crystal Structure of the cross-restricted T18A TCR and HLAB8101 bound to HIV-1 Gag TL9… · the same entry in another collection · chain A against A, 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 I3ZN85
- Every structure of UniProt P61769
- Every structure of UniProt P03367
- Elsewhere: RCSB PDB 7DZM · PDBe 7DZM · UniProt I3ZN85 · UniProt P61769 · UniProt P03367
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