Research workbench
Human 199.16 TCR in complex with melan-A/MART-1 (26-35) peptide and HLA-A2
Analyse Human 199.16 TCR in complex with melan-A/MART-1 (26-35) peptide and HLA-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NQK
- 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, A0A075B6X0, A0A1B0GUM0, A0A5B3, A0A0C4ZKA8
- Ligands
- NA
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 24% helix, 36% strand | P01892 |
| L | Beta-2-microglobulin | protein | 100 | 0% helix, 44% 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 alpha joining 45,T-cell receptor alpha chain C region | protein | 197 | 2% helix, 41% strand | A0A075B6T6, A0A075B6X0, A0A1B0GUM0 |
| B | T-cell receptor beta variable 19,TRB protein | protein | 242 | 4% helix, 40% strand | A0A5B3, A0A0C4ZKA8 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.71 | 0.75 | 81 | NA |
| 2 | 644 | 0.68 | 0.77 | 67 | empty |
| 3 | 240 | 0.56 | 0.78 | 44 | empty |
| 4 | 91 | 0.52 | 0.84 | 20 | empty |
| 5 | 175 | 0.48 | 0.77 | 32 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2030 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1493 Ų buried · 24 hydrogen bonds · protein-protein
- H–P · 916 Ų buried · 17 hydrogen bonds · protein-protein
- H–A · 471 Ų buried · 3 hydrogen bonds · protein-protein
- H–B · 402 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5NQK · human 199.16 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 A0A075B6X0
- Every structure of UniProt A0A1B0GUM0
- Every structure of UniProt A0A5B3
- Every structure of UniProt A0A0C4ZKA8
- Elsewhere: RCSB PDB 5NQK · PDBe 5NQK · UniProt P01892 · UniProt P61769 · UniProt A0A075B6T6 · UniProt A0A075B6X0 · UniProt A0A1B0GUM0 · UniProt A0A5B3 · UniProt A0A0C4ZKA8
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