Research workbench
Crystal structure of the disulfide engineered HLA-A0201 molecule devoid of peptide (annealed)
Analyse Crystal structure of the disulfide engineered HLA-A0201 molecule devoid of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TDR
- 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
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MHC class I antigen | protein | 275 | 28% helix, 39% strand | F6IQS1 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.79 | 0.81 | 99 | empty |
| 2 | 744 | 0.70 | 0.77 | 66 | empty |
| 3 | 243 | 0.60 | 0.79 | 40 | EDO |
| 4 | 91 | 0.51 | 0.83 | 23 | empty |
| 5 | 96 | 0.50 | 0.82 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1400 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1391 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 653 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6TDR · Crystal structure of the disulfide engineered HLA-A0201 molecule devoid of peptide… · 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 D 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 6TDR · PDBe 6TDR · UniProt F6IQS1 · UniProt P61769
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