MolNFT v1 · #70526 · protein
Crystal structure of HLA-B*4103 in complex with a 16MER self-peptide derived from heterogeneous nuclear ribonucleoproteins C1/C2
3LN4 · HLA class I histocompatibility antigen, B-41 alpha chain: “Crystal structure of HLA-B*4103 in complex with a 16MER self-peptide derived from heterogeneous nuclear…”. X-ray diffraction, 6 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 3LN4
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-41 alpha chain; Beta-2-microglobulin; 16-mer…
- UniProt
- P30479, P61769, P07910
- Pockets
- 6 · best druggability 0.68
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-41 alpha chain | protein | 274 | 27% helix, 39% strand | P30479 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | 16-mer peptide from heterogeneous nuclear ribonucleoproteins C1/C2 | protein | 8 | 0% helix, 0% strand | P07910 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, B
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 | 604 | 0.68 | 0.77 | 53 | empty |
| 2 | 138 | 0.62 | 0.85 | 22 | empty |
| 3 | 130 | 0.43 | 0.76 | 20 | empty |
| 4 | 98 | 0.41 | 0.77 | 24 | empty |
| 5 | 77 | 0.39 | 0.78 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1275 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 791 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3LN4 · Crystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from… · 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
- P07910 · AlphaFold monomer V2.0 prediction for heterogeneous nuclear ribonucleoproteins C1/C2… · a predicted model of the same protein · chain C against A, TM-score 0.49
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 P30479
- Every structure of UniProt P61769
- Every structure of UniProt P07910
- Elsewhere: RCSB PDB 3LN4 · PDBe 3LN4 · UniProt P30479 · UniProt P61769 · UniProt P07910
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