Research workbench
Crystal structure of a citrulline peptide variant of the minor histocompatibility peptide ha-1 in complex with HLA-A2
Analyse Crystal structure of a citrulline peptide variant of the minor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FT2
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Citrulline…
- UniProt
- P01892, P61769
- Ligands
- CIR
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 27% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| P | Citrulline variant ha-1 peptide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.68 | 0.77 | 60 | empty |
| 2 | 82 | 0.51 | 0.84 | 19 | CIR |
| 3 | 90 | 0.43 | 0.79 | 19 | empty |
| 4 | 50 | 0.37 | 0.81 | 15 | empty |
| 5 | 66 | 0.34 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1371 Ų buried · 20 hydrogen bonds · protein-protein
- A–P · 797 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3FT2 · Crystal Structure of a citrulline peptide variant of the minor histocompatibility 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 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3FT2 · PDBe 3FT2 · UniProt P01892 · UniProt P61769
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