Research workbench
Crystal structure of the disulfide engineered HLA-A0201 molecule without peptide bound after nacl wash
Analyse Crystal structure of the disulfide engineered HLA-A0201 molecule without… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TDS
- Type
- protein
- Length
- 750 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
- NA, CL
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MHC class I antigen | protein | 275 | 28% helix, 40% strand | F6IQS1 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- NA · Sodium ion · metal · 15 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C
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 | 903 | 0.78 | 0.81 | 95 | CL |
| 2 | 476 | 0.68 | 0.79 | 46 | NA |
| 3 | 175 | 0.55 | 0.80 | 31 | CL |
| 4 | 189 | 0.54 | 0.79 | 34 | CL, NA |
| 5 | 102 | 0.48 | 0.80 | 20 | EDO, CL |
Interfaces
3 interfaces between chains.
- C–D · 1346 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1333 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 506 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6TDS · Crystal structure of the disulfide engineered HLA-A0201 molecule without peptide bound… · the same entry in another collection · chain A against A, 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
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 6TDS · PDBe 6TDS · UniProt F6IQS1 · UniProt P61769
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