Research workbench
Crystal structure of HLA-B*4402 in complex with the F3A mutant of a self-peptide derived from DPA*0201
Analyse Crystal structure of HLA-B*4402 in complex with the F3A mutant of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L3D
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-44 alpha chain; Beta-2-microglobulin; Peptide…
- UniProt
- P30481, P61769, Q95HB9
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-44 alpha chain | protein | 276 | 26% helix, 40% strand | P30481 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Peptide from HLA-DPA1 protein | protein | 9 | 0% helix, 0% strand | Q95HB9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.69 | 0.77 | 54 | empty |
| 2 | 165 | 0.49 | 0.77 | 30 | empty |
| 3 | 72 | 0.39 | 0.79 | 17 | empty |
| 4 | 70 | 0.37 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1286 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 907 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3L3D · Crystal structure of HLA-B*4402 in complex with the F3A mutant of a self-peptide derived… · 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 P30481
- Every structure of UniProt P61769
- Every structure of UniProt Q95HB9
- Elsewhere: RCSB PDB 3L3D · PDBe 3L3D · UniProt P30481 · UniProt P61769 · UniProt Q95HB9
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