MolNFT v1 · #146546 · protein
The complex among DMF5(ALPHA-D26Y, alpha-Y50A,BETA-L98W) TCR, human class I MHC HLA-A2 and mart-1(26-35)(A27L) peptide
6DKP · HLA class I histocompatibility antigen, a-2 alpha chain: “The complex among DMF5(ALPHA-D26Y, alpha-Y50A,BETA-L98W) TCR, human class I MHC HLA-A2 and…”. X-ray diffraction, 8 pockets (best druggability 0.75). MolNFT v1 #146546 on…
- PDB
- 6DKP
- Type
- protein
- Length
- 818 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, Q16655, A0A075B6T6, P01848, A0A1B0GXE1, K7N5M4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 12% 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, 39% strand | P01892 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Melanoma antigen recognized by T-cells 1 | protein | 10 | 0% helix, 0% strand | Q16655 |
| D | DMF5 T-cell receptor alpha chain fusion | protein | 192 | 5% helix, 46% strand | A0A075B6T6, P01848 |
| E | DMF5 T-cell receptor beta chain fusion | protein | 242 | 7% helix, 48% strand | A0A1B0GXE1, K7N5M4 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.75 | 0.93 | 27 | empty |
| 2 | 984 | 0.72 | 0.76 | 81 | empty |
| 3 | 658 | 0.71 | 0.79 | 54 | empty |
| 4 | 134 | 0.52 | 0.81 | 27 | empty |
| 5 | 133 | 0.50 | 0.80 | 25 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2263 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1325 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 910 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 604 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 435 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6DKP · The complex among DMF5(alpha-D26Y, alpha-Y50A,beta-L98W) TCR, human Class I MHC HLA-A2… · 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
- P01848 · AlphaFold monomer V2.0 prediction for T cell receptor alpha chain constant (P01848) · a predicted model of the same protein · chain D against A, TM-score 0.41
- Q16655 · AlphaFold monomer V2.0 prediction for melanoma antigen recognized by T-cells 1 (Q16655) · a predicted model of the same protein · chain C against A, TM-score 0.34
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 Q16655
- Every structure of UniProt A0A075B6T6
- Every structure of UniProt P01848
- Every structure of UniProt A0A1B0GXE1
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 6DKP · PDBe 6DKP · UniProt P01892 · UniProt P61769 · UniProt Q16655 · UniProt A0A075B6T6 · UniProt P01848 · UniProt A0A1B0GXE1 · UniProt K7N5M4
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