MolNFT v1 · #128145 · protein
Human 199.54-16 TCR in complex with melan-A/MART-1 (26-35) peptide and HLA-A2
5NHT · HLA class I histocompatibility antigen, a-2 alpha chain: “Human 199.54-16 TCR in complex with melan-A/MART-1 (26-35) peptide and HLA-A2”. X-ray diffraction, 3 ligands (K, SCN, CL), 14 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 5NHT
- Type
- protein
- Length
- 824 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; Melanoma…
- UniProt
- P01892, P61769, A0A075B6T6, K7N5N2, A0A5B3, A0A0C4ZKA8
- Ligands
- K, SCN, CL
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 26% helix, 36% strand | P01892 |
| L | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| P | Melanoma antigen recognized by T-cells 1 | protein | 10 | 0% helix, 0% strand | — |
| A | T-cell receptor alpha variable 12-2,T-cell receptor, SP3.4 alpha chain | protein | 197 | 3% helix, 42% strand | A0A075B6T6, K7N5N2 |
| B | T-cell receptor beta variable 19,TRB protein | protein | 242 | 4% helix, 37% strand | A0A5B3, A0A0C4ZKA8 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains H, L
- SCN · Thiocyanate ion · ion · chains H, L
- CL · Chloride ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.71 | 0.75 | 94 | empty |
| 2 | 680 | 0.70 | 0.77 | 66 | K |
| 3 | 306 | 0.61 | 0.79 | 47 | empty |
| 4 | 57 | 0.50 | 0.86 | 18 | empty |
| 5 | 125 | 0.46 | 0.78 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2033 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 1485 Ų buried · 22 hydrogen bonds · protein-protein
- H–P · 908 Ų buried · 16 hydrogen bonds · protein-protein
- H–A · 479 Ų buried · 4 hydrogen bonds · protein-protein
- H–B · 412 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5NHT · human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2 · the same entry in another collection · chain H against H, 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 0.98
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
- Every structure of UniProt A0A075B6T6
- Every structure of UniProt K7N5N2
- Every structure of UniProt A0A5B3
- Every structure of UniProt A0A0C4ZKA8
- Elsewhere: RCSB PDB 5NHT · PDBe 5NHT · UniProt P01892 · UniProt P61769 · UniProt A0A075B6T6 · UniProt K7N5N2 · UniProt A0A5B3 · UniProt A0A0C4ZKA8
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