MolNFT v1 · #167488 · protein
T4H2 T cell receptor bound to HLA-A2 presenting GP100 peptide (itdqvpfsv)
6VMA · MHC class I antigen, a-2 alpha chain: “T4H2 T cell receptor bound to HLA-A2 presenting GP100 peptide (itdqvpfsv)”. X-ray diffraction, 11 pockets (best druggability 0.72). MolNFT v1 #167488 on GenesisL1: 3D structure, binding sites…
- PDB
- 6VMA
- Type
- protein
- Length
- 824 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen, a-2 alpha chain; Beta-2-microglobulin; T4H2 T cell receptor alpha…
- UniProt
- A0A5B8RNS7, P61769, P40967
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen, a-2 alpha chain | protein | 275 | 27% helix, 42% strand | A0A5B8RNS7 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| D | T4H2 T cell receptor alpha chain | protein | 201 | 3% helix, 46% strand | — |
| E | T4H2 T cell receptor beta chain | protein | 239 | 5% helix, 47% strand | — |
| C | Melanocyte protein pmel | protein | 9 | 0% helix, 0% strand | P40967 |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.72 | 0.76 | 91 | empty |
| 2 | 622 | 0.68 | 0.77 | 60 | empty |
| 3 | 164 | 0.52 | 0.79 | 34 | empty |
| 4 | 141 | 0.49 | 0.79 | 24 | empty |
| 5 | 116 | 0.46 | 0.79 | 23 | empty |
Interfaces
4 interfaces between chains.
- D–E · 2077 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1349 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 864 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 255 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6VMA · T4H2 T cell receptor bound to HLA-A2 presenting gp100 peptide (ITDQVPFSV) · the same entry in another collection · chain B against B, 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 0.99
- P40967 · AlphaFold monomer V2.0 prediction for melanocyte protein pmel (P40967) · a predicted model of the same protein · chain C against A, TM-score 0.46
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 A0A5B8RNS7
- Every structure of UniProt P61769
- Every structure of UniProt P40967
- Elsewhere: RCSB PDB 6VMA · PDBe 6VMA · UniProt A0A5B8RNS7 · UniProt P61769 · UniProt P40967
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