MolNFT v1 · #142996 · protein
Crystal structure of DMF5 TCR bound to HLA-A2 presenting synthetic peptide smlgigivpv
6AM5 · HLA class I histocompatibility antigen, a-2 alpha chain: “Crystal structure of DMF5 TCR bound to HLA-A2 presenting synthetic peptide smlgigivpv”. X-ray diffraction, 9 pockets (best druggability 0.72). MolNFT v1 #142996 on GenesisL1…
- PDB
- 6AM5
- Type
- protein
- Length
- 816 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; Beta-2-microglobulin…
- UniProt
- P01892, P61769
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 26% helix, 38% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Ser-met-leu-gly-ile-gly-ile-val-pro-val | protein | 10 | 0% helix, 0% strand | — |
| D | DMF5 TCR alpha chain | protein | 189 | 2% helix, 48% strand | — |
| E | DMF5 TCR beta chain | protein | 242 | 7% helix, 48% 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 | 1129 | 0.72 | 0.76 | 83 | empty |
| 2 | 531 | 0.68 | 0.78 | 51 | empty |
| 3 | 113 | 0.52 | 0.82 | 20 | empty |
| 4 | 154 | 0.49 | 0.78 | 30 | empty |
| 5 | 77 | 0.44 | 0.81 | 20 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2137 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1447 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 875 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 619 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 373 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6AM5 · Crystal structure of DMF5 TCR bound to HLA-A2 presenting synthetic peptide SMLGIGIVPV · 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6AM5 · PDBe 6AM5 · UniProt P01892 · UniProt P61769
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