MolNFT v1 · #164920 · protein
Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one gm dipeptide in the a pocket and one gm dipeptide in the F pocket.
6TDQ · MHC class I antigen: “Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one gm dipeptide in the a…”. X-ray diffraction, 1 ligand (CL), 11 pockets (best druggability 0.77). MolNFT v1 #164920 on…
- PDB
- 6TDQ
- Type
- protein
- Length
- 758 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin
- UniProt
- F6IQS1, P61769
- Ligands
- CL
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MHC class I antigen | protein | 279 | 27% helix, 39% strand | F6IQS1 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.77 | 0.80 | 97 | empty |
| 2 | 811 | 0.72 | 0.77 | 73 | empty |
| 3 | 153 | 0.54 | 0.80 | 30 | EDO |
| 4 | 112 | 0.52 | 0.82 | 19 | EDO |
| 5 | 140 | 0.47 | 0.78 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1376 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1346 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 615 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6TDQ · Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GM… · 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
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 F6IQS1
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6TDQ · PDBe 6TDQ · UniProt F6IQS1 · UniProt P61769
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