Research workbench
Three dimensional structure of a peptide extending out one end of a class I MHC binding site
Analyse Three dimensional structure of a peptide extending out one end of a class I MHC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CLR
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class I histocompatibility antigen (HLA-a 0201) (alpha chain); Beta 2-microglobulin…
- UniProt
- P01892, P61769, P27797
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Class I histocompatibility antigen (HLA-a 0201) (alpha chain) | protein | 275 | 28% helix, 40% strand | P01892 |
| B, E | Beta 2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Decameric peptide from calreticulin | protein | 10 | 0% helix, 0% strand | P27797 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.70 | 0.78 | 55 | empty |
| 2 | 550 | 0.66 | 0.77 | 55 | empty |
| 3 | 157 | 0.48 | 0.77 | 29 | empty |
| 4 | 144 | 0.47 | 0.77 | 20 | empty |
| 5 | 62 | 0.43 | 0.82 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1415 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1395 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 912 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 892 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2CLR · Three dimensional structure of a peptide extending out one end of a class I MHC binding… · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P27797 · AlphaFold monomer V2.0 prediction for calreticulin (P27797) · a predicted model of the same protein · chain C against A, TM-score 0.39
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 P27797
- Elsewhere: RCSB PDB 2CLR · PDBe 2CLR · UniProt P01892 · UniProt P61769 · UniProt P27797
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